The Science of it All

Chromosome Fusion 2 Debunked

A popular claim is that the genomes of chimpanzees, or chimps (Pan troglodytes), and humans (Homo sapiens) are nearly identical. This paradigm is based primarily on cherry-picked highly homologous DNA and protein sequences

One of the most popularized molecular arguments for human-primate evolution is the hypothetical prehistoric head-to-head fusion of two primate chromosomes (corresponding to 2A and 2B in chimpanzee) to form human chromosome number 2. Much of the research supporting this hypothetical model is derived from indirect evidence of DNA hybridization and chromosomal staining techniques. These techniques provide only approximate estimates of sequence similarity, with hybridization-based analyses being more accurate than the analysis of stained chromosomal bands. These were the first attempts and today’s scientists stick to the initial faulty conclusions with a vengeance.

DNA sequencing technologies have improved and have become considerably more proficient and automated. As a result, DNA similarity research between humans and chimps is able to utilize actual DNA base-pair information on a larger scale. As noted by Marks, it is important to understand that since only four DNA bases exist in all genomes, any two random stretches of DNA of the same length will always be about 25% identical. In other words, the starting point in human–chimp DNA comparisons is not zero, but 25%.[i]

Popular reviews on this subject often include a simplified drawing depicting how the putative fusion of two small acrocentric[ii] ape-like precursor chromosomes could have fused end-to-end to form the larger human chromosome 2, as shown in figure 1.


Of the two genomic features that are claimed to support the fusion model, the primary evidence used is the presence of a reputed (not able to prove except by speculation) fusion site. This site is located in a pericentric region (meaning it is close to the present functional centromere) on the long arm of human chromosome 2. The DNA sequence at this location is the supposed evidence of a head-to-head telomeric fusion of two acrocentric chromosomes.

Miller cites as proof for the fusion states only that “Human chromosome two is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes” and provides no evidence for this conclusion. Fairbanks offers more detail and claims that there appears (or rather it seems like based upon what I want to believe) to exist a fusion site involving a set of 158 telomere sequences, and, of the 158 repeats, he notes only 44 sets can be manipulated to achieve perfect telomere consensus sequences. Another example of the same claim from a book popularizing human evolution is as follows: “The DNA sequences in the human chromosome are exactly as expected from this scenario. Telomeres consist of many repeats of the nucleotide sequence TTAGGG, and at the fusion point of the human chromosome, where the two telomeres fused, this sequence is found ‘head to head’. The functional centromere in chromosome 2 lines up with the chimpanzee chromosome 2p13 chromosomal centromere. The remains of the redundant centromere from one of the ancestral ape chromosomes can also be found.”[iii]

We need to briefly clarify the structure and nature of telomeres as to what would be expected if such a fusion event occurred. In so doing, we will even take into account the accepted evolutionary presuppositions and timelines related to such an event. (Just to show you how bad science is passed off as ‘proof’).

Telomeres are typically found at the ends of linear eukaryotic chromosomes and confer stability by preventing fusion via a ‘capping’ function. The telomere region involves a complex and dynamic framework of DNA motif repeats, structural loops, structural and functional RNAs and a wide variety of proteins.[iv]

The consensus telomere motif in humans, chimps, apes, and mammals in general, is (TTAGGG)n and typically occurs in perfect tandem for stretches of DNA from about 10 to 15 kb (10,000 to 15,000 bases) and contains 1,667 to 2,500 telomere repeats at each chromosome end. In a head-to-head fusion of two chromosomes, we would expect at least 5,000 bases of (TTAGGG)n repeats in tandem, albeit in a slightly degenerate state, given a supposed ~1 to 5 million years of evolution since the fusion event occurred. At the point of fusion, we would also expect the orientation of the plus-strand repeat to change to the reverse complement (CCCTAA)n, which should also occur in near-perfect tandem for approximately 5,000 or more bases.

One of the major problems with the fusion model is that, within the 10 to 30 kb window of DNA sequence surrounding the hypothetical fusion site, a glaring paucity of telomeric repeats exist that appear mostly as independent monomers, not tandem repeats. Based on the predicted model, thousands of intact motifs in tandem should exist. For the TTAGGG repeat to the left of the fusion site, less than 35 motifs exist, a normal human telomere would typically have 1667 to 2500.iv For the CCCTAA reverse complement sequence, to the right of the fusion site, less than 150 telomere motifs can be found. Another problem with these two motifs, is that their occurrences are found scattered throughout both sides of the fusion site where they would not be expected. In other words, both the forward and reverse complement of the telomere motif populate both sides of the fusion site.

The only evolutionary research group to seriously analyze the actual fusion site DNA sequence data in detail were confounded by the results which showed a lack of evidence for fusion—a genomic condition for this region which they termed ‘degenerate’.[v] In attempting to correlate rates of evolutionary change with the extreme degeneracy observed in the putative fusion region, they claimed that the “head-to-head arrays of repeats at the fusion site have degenerated significantly from the near perfect arrays of (TTAGGG)n found at telomeres.” They also stated, “if the fusion occurred within the telomeric repeat arrays less than ~6 Ma, why are the arrays at the fusion site so degenerate?” The actual data indicates that perhaps the only thing that is degenerate is the evolutionary dogma surrounding the fusion model.


The key papers that report DNA sequence similarities do so using multiple levels of biological sample and/or data preselection. In most cases, the authors only report the ‘best of the best’ data—a form of dogma-driven bioinformatic cherry picking. For example, only the protein-coding gene sequences of preselected highly similar DNA are often used—guaranteeing high levels of similarity.[vi]


In retrospect, it appears that the early reports of human–chimp DNA similarity, based on reassociation kinetics, has set a ‘98 to 99% Gold Standard’ whereby the results of subsequent DNA sequence-based research conformed accordingly, even though the buried and obfuscated data related to these reports said otherwise. Such conformity to largely unspoken academic rules is typically required to achieve success in grantsmanship, publishing, tenure, and job security in general.[vii]

The candid quote below from a fairly recent evolutionary paper states the issue very clearly.

“However, with both amount of data and number of studies increasing, the crux of the matter emerges. Regardless of the type of phylogenetically informative data chosen for analysis, the evolutionary history of humans is reconstructed differently with different sets of data.”[viii]

The common but false assumption that repetitive DNA (‘junk’ DNA) is irrelevant is prevalent. By using techniques similar to those used in making comparisons between humans and chimps, human DNA also turns out to be, roughly, estimated to be about 35% identical to daffodil DNA, but it does not follow that we are physically 35% daffodil.i Chimp and human share greater DNA similarities than either chimp or human compared to a daffodil, but putting a precise measure on the similarity is not a trivial task, and the published numbers are clearly misleading due to their beguiling appearance of simplicity, the unstated assumptions required to produce them, and the illusion of precision that they convey.


If you are anything like me, your first question is what do all the colors mean? To verify the BLAT results and to identify homologous sites in the chimpanzee genome, the BLASTN algorithm was used (with no masking or gap extension) for comparisons between the 798-bp core 2qfus sequence and the most recent builds of the human (v 37.1) and chimp (v 2.1) genomes maintained at NCBI ( Although the BLASTN query against the human genome was more data intensive than the index-based BLAT search, the results produced a total of 85 significantly placed hits on all human chromosomes except chromosomes 13, 16 and 17 (1–12, 14, 15, 18–22, X and Y). While the number of hits was reduced, compared to BLAT, more chromosomes with homologous sites were identified with the BLASTN search because of the more direct nature of the algorithm (figure 3). Interestingly, human chromosomes 2, 16, 21 and 22 were peppered with the ‘fusion site’ sequence over the length of their entire euchromatic landscape (figure 3). Pretty impressive scientific mumbo-jumbo isn’t it. This is what it means:

When the 798-bp core fusion sequence was BLASTN queried against the chimpanzee genome, the significantly placed hit count was reduced to 19, only 22% of the amount observed in the human genome. This is a startling find in light of the wide-spread claims that the human and chimpanzee genomes contain DNA sequence that is supposedly 96 to 98% similar. This claim is perhaps related to the fact that the human genome was used as a scaffold to build the chimpanzee genome.[ix] In addition, the human-chimp hit locations did not show strong synteny, as only 13 of the 19 hits (68%) shared visually similar locations in the genome (on chimpanzee chromosomes 1, 2B, 8, 9, 12, 14, 15, 18, 20 and 22).

The most startling outcome of this analysis is that the fusion site did not align with chimp chromosome 2A, one of the supposed pre-fusion precursors. Furthermore, the alignment at two locations on chromosome 2B, an internal euchromatic site and the telomere region of its long arm, did not match predicted fusion-based locations based on the fusion model. If the fusion model was credible, this should have produced an alignment with the telomeric region on chimpanzee 2B on the short arm.


If published research statements concerning highly selective cherry-picked data are taken at face value, to conclude that human and chimpanzee DNA are 94% (or greater) similarity is still seriously misleading. The problem is that we tend to think of DNA sequence as a human-written language, in standard linear format similar to the English 26 letter alphabet. Such reasoning evaluates differences as if one would line up parallel written texts. Two books written by humans that are 98% similar are essentially the same book. Evolutionists often use this analogy, but it is completely inappropriate. The DNA four-letter alphabet code that designates twenty different amino acids by codons (triplet bases of specific sequences) considers only the small fraction of the genome that actually codes for protein.

The rest of the genome involves many other DNA code types that includes for regulatory function, nuclear matrix attachment features, nuclear arrangement and packaging, and a whole diversity of two-and three-dimensional structures. The extreme diversity of informational code in the genome also occurs, not only in multiple abstract layers of extreme informational complexity, but also in both two-and three-dimensional formats (topology-based information) that are interactive with linear-based sequence information. Many linear-based genomic codes (genomic features) also contain multiple levels of meaning and are far beyond the complexity of the human alphabet or any man-made, high-level, object-oriented computer code.[x]

Next we will deal with VIGE (variation-inducing genetic elements) and how biological information is inherited which will take us back to and update a previous series and information and what it is. If you wish to review that information it can be found at:


If at any time you feel over your head in information and need something explained further, please drop me a line at and I’ll do my best to explain things further for you.


[i] Marks, J., What it Means to Be 98% Chimpanzee: Apes, People and Their Genes, Berkeley and Los Angeles, CA, University of California Press, 2002

[ii] Acrocentric chromosome has one arm that is considerably shorter than the other arm. The ‘acro-’ in ‘acrocentric’ refers to the Greek word for ‘peak’. The human genome contains five acrocentric chromosomes: 13, 14, 15, 21 and 22. The naming system of chimpanzee chromosomes ‘2A’ and ‘2B’ was first used by McConkey, E.H., Orthologous numbering of great ape and human chromosomes is essential for comparative genomics, Cytogenet Genome Research105:157–158, 2004. Prior to that, the chimpanzee chromosomes were numbered according to size, as is the system used for all other species.

[iii] Fairbanks, D.J., Relics of Eden, Quotations and analyses are in reference to Chapter 1, Fusion, Prometheus Books, Amherst, N.Y., pp. 17–30, 2007

[iv] Tomkins, J. and Bergman, J., Telomeres: implications for aging and evidence for intelligent design, J. Creation 25(1):86–97, 2011.

[v] Fan, Y. et al., Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes, Genome Research 12:1651–1662, 2002.

[vi] Britten, R.J., Divergence between samples of chimpanzee and human DNA sequences is 5% counting indels, Proceedings of the National Academy of Sciences 99:13633–13635, 2002.

[vii] See Bergman, J., Slaughter of the Dissidents: The Shocking Truth About Killing the Careers of Darwin Doubters, Leafcutter Press, Southworth, WA, 2008.

[viii] Ebersberger, I. et al., Mapping human genetic ancestry, Molecular Biology and Evolution 24:2266–2276, 2007.

[ix] The Chimpanzee Sequencing and Analysis Consortium, Initial sequence of the chimpanzee genome and comparison with the human genome, Nature437:69–87, 2005.

[x] Barash, Y. et al., Deciphering the splicing code, Nature 465:53–59, 2010.


6 thoughts on “Chromosome Fusion 2 Debunked

  1. Hi Larry, I sent you an email back in June 2016 disputing the major objections to chromosome fusion. You can check out my posts on the topic at

    Happy to have a conversation here or over there – whatever is convenient to you. I notice your offer to explain things to other people and I’m hoping if positions were reversed you were able to accept correction.


    1. Hi, rooif. I am truly sorry that I missed your original post. During that time, I was traveling back and forth between Big Spring, Tx and Dallas because my youngest daughter had a tumor in her cheekbone. The 4 hour surgery with two doctors ended up being 12 hours with eight doctors. Then back and forth for followups. So I apologize. Could you be so kind as to restate it for me and I’ll restudy the chromosome fusion. I read about 6 articles on your site, so I can lay out, I hope a worthy rebuttal, so we can engage in a discussion. LEM

  2. Thanks Larry,

    Sorry to hear about your daughter – I hope she is okay! Funnily enough, I’m actually writing from hospital at the moment: I’m almost halfway through a stem cell transplant after being diagnosed with AML a few months back.

    I’m not sure what you mean by “restate my case”, so I thought I’d just go through each point as you present it in your post:

    “This paradigm is based primarily on cherry-picked highly homologous DNA and protein sequences”

    I wrote a paper on this: performed my own comparisons and submitted it to AiG. I treated indels in a relatively conservative way, and came to an overall result of 96.90% identity. It was this submission that caused Jeff Tomkins to revise his 70% figure up to 88%. My “Is 1% a Myth?” post goes into detail about why his new figure is incorrect.

    Interestingly, human chromosomes 2, 16, 21 and 22 were peppered with the ‘fusion site’ sequence over the length of their entire euchromatic landscape.

    The ‘fusion site’ can only be said to be found elsewhere if it spans both sides of the precise fusion point. Otherwise, all you are really saying is that “we found one side of the fusion on other chromosomes” . That’s not surprising, given that each side of the fusion resembles the subtelomeric sequences found on other chromosomes.

    The BLASTN hits in your image contain very low quality matches – there are many green and purple hits (low scoring), but if you tighten the parameters to include high scoring hits only, this is what you get:

    The red hits on this image are from the right hand side of the fusion site, while the blue hits are from the left. There are no hits than include the precise (i.e. single locus) fusion point. As you can see, all of the hits are found adjacent to the telomeres.

    The head-to-head configuration found on chromosome 2 is the only such hit on either the human or the chimpanzee genomes.

    Also – just FYI – the reason you get less hits on the chimpanzee genome in your image is because BLAT was used instead of BLASTN. BLAT masks repeat regions and therefore will “result in missing hits when you are searching for sequences in repeats”.

    1. Hi roooir, I am sorry to hear about your needing a stem cell transplant. I certainly hope and pray for your recovery. I must tip my hat to you in that you certainly appear to know more about the subject matter than I do. I certainly would like to be able to pick your mind on this and some other subjects if you have no objections. As it is I would like to just lay out what appears to each others point of view. It seems to me that you would be classified as an ‘evolutionist’ believing that humans are related to the apes through years of mutational natural selection. I would claim that I am a believer in Intelligent Design with the ultimate designer being our Lord. As I have written before I still have problems with believing in a Young Age Earth: “I am still not 100% convinced due to some 55 years of indoctrination into the evolutionists point of view. An earth that is only 10,00 to 6,000 years old just seems incredibly dumb to believe if you have fallen hook, line and sinker for the prevalent mode being taught daily to the students in our schools.” But many things I research between secular and Biblical geologists has me leaning toward a YAE, but …….. Hope you get to feeling better, My daughter just needs one more operation to remove a titanium piece they used to create an eye orbit, the bone is growing in just fine. Until later. LEM

  3. human DNA also turns out to be, roughly, estimated to be about 35% identical to daffodil DNA

    Purely for curiosity, I tried to find a source for this in Jonathan Mark’s book. Turns out it’s a completely made-up number:

    Thus, if you compare the DNA of a human and a daffodil, the
    25% mark is actually the zero mark, and since humans and daffodils
    do share a common ancestry, you would expect them to be generally
    more similar than 25%. Say, about 35%.

    What’s I find interesting is how a quick Google search for “35% daffodil DNA” shows many hits that consider this a fact.

  4. Every weekend i used to pay a quick visit this web page,
    for the reason that i want enjoyment, for the reason that this
    this site conations really fastidious funny stuff too.

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