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Frank Visser, graduated as a psychologist of culture and religion, founded IntegralWorld in 1997. He worked as production manager for various publishing houses and as service manager for various internet companies and lives in Amsterdam. Books: Ken Wilber: Thought as Passion (SUNY, 2003), and The Corona Conspiracy: Combatting Disinformation about the Coronavirus (Kindle, 2020).

The Human Chromosome 2 Fusion

A Genetic Smoking Gun and
the Creationist Response

Frank Visser / ChatGPT

One of the most compelling pieces of evidence for human evolution is the fusion of human chromosome 2. It is a textbook example of how molecular genetics can illuminate our shared ancestry with other primates. And yet, despite its clarity, this evidence has not gone unchallenged. Creationist thinkers, long invested in denying common descent, have responded to the chromosome 2 fusion with a mixture of denial, distortion, and pseudoscientific reinterpretation. This essay examines the science behind the chromosome 2 fusion, how it supports evolutionary theory, and how creationist apologists have attempted to neutralize its implications—often at the cost of intellectual integrity.

The Scientific Story: A Fusion Written in Our DNA

Humans have 46 chromosomes (23 pairs), while our closest relatives—chimpanzees, bonobos, and gorillas—have 48 (24 pairs). This discrepancy once posed a potential problem for evolutionary theory. If humans and other apes share a common ancestor, why the different chromosome counts? The mystery was solved with the discovery that human chromosome 2 is the result of an end-to-end fusion of two ancestral ape chromosomes. Geneticists identified several lines of evidence:

• Telomere remnants: Normally, telomeres cap the ends of chromosomes. In human chromosome 2, researchers found telomeric sequences in the middle, precisely where the fusion would have occurred
• Two centromeres: Chromosomes have a single centromere used in cell division. Chromosome 2 has a primary active centromere and remnants of a second, inactivated centromere—exactly what you'd expect if two chromosomes fused.
• Gene synteny: The genes on human chromosome 2 are arranged in an order that matches two separate chromosomes in chimpanzees and other great apes.

These findings, first confirmed in the 1990s and further refined since, decisively support the idea that humans share a common ancestor with other great apes. The fusion likely occurred in a hominid ancestor around 4 to 5 million years ago and became fixed in the population.

Creationist Reactions: Denial and Damage Control

Rather than accept the clear implications of this evidence, young-Earth and intelligent design (ID) creationists have responded with a variety of tactics aimed at sowing doubt or redefining the terms of the debate. These responses fall into several predictable patterns:

1. Minimizing the Significance

Creationists like Ken Ham or those at Answers in Genesis often downplay the fusion, suggesting it's merely an “interesting” genetic event, not proof of common ancestry. They argue that even if fusion occurred, it doesn't demonstrate evolution—ignoring the fact that such a specific fusion would be astronomically unlikely to occur independently in two lineages. The precise match between human chromosome 2 and chimp chromosomes 2a and 2b isn't just suggestive of common descent—it practically demands it.

2. Redefining “Design”

ID proponents, such as those at the Discovery Institute, occasionally accept that a fusion occurred but argue that it was intelligently designed. They suggest that the fusion served a functional or regulatory purpose, perhaps as part of a “designed” human genome. In this view, the fusion is not a random event, but a purposeful rearrangement by an intelligent agent. This “heads I win, tails you lose” argument attempts to shield design from falsifiability: every feature, no matter how accidental or evolutionary it appears, is retroactively declared purposeful. This tactic moves the discussion from science to metaphysics. It replaces testable hypotheses with unfalsifiable assertions and retreats into the realm of mystery whenever confronted with solid evidence.

3. Attacking the Evidence

Some creationists claim that the fusion site is not a true telomere-telomere fusion. They argue that the telomeric sequences in the middle of chromosome 2 are degenerate or too short to be real. But this is a red herring. Telomeric sequences are known to degrade over time, especially when they are internalized by a fusion. The presence of any remnants, especially in such a consistent pattern, still supports the fusion model.

Likewise, some critics suggest that the second centromere is merely a centromeric-like region and not definitive. However, the sequence contains enough similarity to known inactive centromeres to establish its identity. Again, this criticism is more rhetorical than substantive.

More recently, creationist apologists have argued that the fusion site is not a "scar" at all but a functional part of a gene—specifically, that it falls within an active transcriptional region called DDX11L2, thereby allegedly disproving that it is a fusion. This claim has been circulated in ID circles and on platforms like Evolution News & Science Today. However, this objection fails for several reasons:

First, the DDX11L2 region is a noncoding RNA pseudogene, with no evidence of a functional protein product. Its transcription does not imply that the fusion site is part of a functionally indispensable gene.

Second, fusion sites becoming embedded in or adjacent to transcribed regions over evolutionary time is not surprising—especially in a large, complex genome like ours. This does not negate the fusion; it simply reflects subsequent genomic remodeling.

Third, detailed sequence analysis shows that the signature of head-to-head telomeric repeats (TTAGGG)n and their reverse complements remains identifiable, even within the DDX11L2 context. The structural footprint of the fusion persists regardless of transcriptional activity nearby.

This creationist argument is another example of quote-mining and cherry-picking technical details in an effort to confuse lay audiences. It reflects a fundamental misunderstanding (or misrepresentation) of how genomic regions can be co-opted, repurposed, or transcribed without invalidating their evolutionary origin.

4. Tomkins and the Creationist Campaign Against Chromosome 2 Fusion

One of the most vocal opponents of the chromosome 2 fusion hypothesis within the creationist community is Jeffrey P. Tomkins, a former geneticist and prominent figure at the Institute for Creation Research (ICR). Tomkins has published a series of articles and pseudo-scientific reports attempting to cast doubt on the fusion site, primarily by reinterpreting genomic data to fit a young-Earth creationist framework. His claims have gained traction in creationist circles but fall apart under critical scrutiny.

Tomkins' Main Arguments

Tomkins has made several core claims about the fusion site:

• The fusion site is too small to represent a real telomere-telomere fusion.
• He notes that the supposed fusion region is only 798 base pairs long and lacks the perfect 6-base TTAGGG telomeric repeats expected in a textbook fusion.
• The fusion site is located within an actively transcribed gene (DDX11L2), so it must be functional.

From this, he concludes that the region must have been purposefully designed and not the result of a fusion event.

The sequence is not unique to humans.

He has implied that similar sequences can be found in other organisms, undermining the idea that this is a distinct fusion event unique to human evolution.

Scientific Refutation

Each of Tomkins' arguments rests on misunderstandings, selective emphasis, or misleading presentation of genetic data. Let's address them in turn:

• On the Size and Degeneracy of the Telomeric Repeats
  Tomkins points out that the internal fusion site contains degenerate telomeric sequences and is shorter than expected. This is true—but entirely consistent with what scientists would expect. Telomeric sequences degrade over time, especially when they are no longer at the ends of chromosomes. The fact that recognizable (albeit degenerate) telomere sequences appear head-to-head in the predicted orientation is the key point—not their perfection.
• On the Fusion Site's Location in a Gene
  As noted earlier, the DDX11L2 region is a noncoding pseudogene, likely a remnant of a once-functional gene family. Its transcription does not mean it performs a necessary biological function, and it certainly doesn't preclude the region from being a relic of a fusion. Moreover, genomic fusions can and do occur within or near genes without negating their identification as fusion sites. Functional annotation is not incompatible with structural mutation.
• On the Alleged Non-Uniqueness of the Sequence
  Tomkins has attempted to argue that similar sequence motifs exist elsewhere in the genome, implying the site is not unique or significant. But this is a classic misuse of sequence similarity. The overall structure, orientation, and synteny of the fusion site—not just the presence of TTAGGG motifs—are what establish its evolutionary origin. In addition, the precise correspondence between chimpanzee chromosomes 2A and 2B and human chromosome 2 in terms of gene order (synteny) and centromeric location is independent corroboration of the fusion.

The Broader Problem

Tomkins' approach exemplifies motivated reasoning—working backwards from a predetermined theological conclusion (humans are specially created) and trying to discredit any data that contradict it. His work is not peer-reviewed in reputable scientific journals, and when scrutinized by experts, it reveals methodological flaws, selective interpretation, and rhetorical sleight of hand rather than genuine scientific critique.

That creationist organizations continue to promote Tomkins' arguments shows how ideology often trumps evidence in these circles. The chromosome 2 fusion is one of the most clear-cut molecular confirmations of common ancestry, and attempts to obscure that reality, however technically dressed, only further discredit creationist science.

Conclusion: An Inconvenient Chromosome

Human chromosome 2 is more than a biological curiosity—it is a genetic fossil bearing witness to our evolutionary heritage. In trying to explain it away, creationists reveal not just the poverty of their alternative models, but the extent to which ideology can distort the interpretation of evidence.

The fusion event does not merely “fit” within the theory of evolution—it confirms a specific prediction. That's not something mythology or dogma can compete with. In the end, chromosome 2 stands as a molecular monument to the unity of life—a truth that cannot be unfused.

Appendix: Refuting Jeffrey Tomkins on Human Chromosome 2 Fusion

Here is a detailed, point-by-point rebuttal of Jeffrey Tomkins' 2015 article “More DNA Evidence Against Human Chromosome Fusion,” which attempts to discredit one of the strongest lines of evidence for human-ape common ancestry.[1]

Jeffrey Tomkins, a creationist geneticist affiliated with the Institute for Creation Research, has written extensively in opposition to the chromosome 2 fusion hypothesis. In his 2015 article, he reiterates several flawed arguments that have become standard in creationist literature. While cloaked in scientific terminology, these claims reflect misinterpretations of genomics, cherry-picked data, and a desire to protect a preordained theological worldview rather than follow the evidence. Below is a point-by-point refutation.

1. “The fusion site is too small and degenerate”

Tomkins argues that the 798 bp fusion site is too short and degraded to be the remnant of two full-length telomeres (each ~5,000–15,000 bp). He also claims the sequence is only ~70% similar to ideal TTAGGG repeats and therefore not a valid fusion.

Rebuttal:

The fusion event is thought to have occurred roughly 4–6 million years ago. Over that time, repetitive sequences are known to degrade, especially when relocated away from protective telomerase activity at chromosome ends.

What matters is not the quantity of perfect repeats, but the unique pattern of head-to-head telomeric repeats in the expected orientation and location—flanked by other hallmarks of chromosomal fusion.

The observed structure is exactly what one would expect from a telomere-telomere fusion that occurred millions of years ago and became fixed in a population.

2. “No satellite DNA (satDNA) found at the fusion site”

Tomkins insists that natural fusions typically involve satDNA (a type of repetitive element), and because satDNA is missing here, this discredits the fusion model.

Rebuttal:

The absence of satDNA is irrelevant to whether a fusion occurred. Most satDNA-mediated fusions involve centromeric fusions, but the human chromosome 2 event is a telomere-telomere fusion, which has a different structure and mechanism.

The original 1991 paper by IJdo et al. explicitly acknowledged the absence of satDNA and proposed a direct head-to-head telomeric fusion—a rarer but documented mechanism.

The fusion type seen in chromosome 2 does not require satDNA, and its absence is entirely consistent with the evolutionary scenario proposed.

3. “The fusion site is located in a functional gene (DDX11L2), so it can't be a fusion”

Tomkins claims the fusion site is now part of an important RNA helicase gene (DDX11L2), suggesting this region was intelligently designed, not a genomic accident.

Rebuttal:

DDX11L2 is a noncoding pseudogene, not a protein-coding helicase gene. It does not produce a functional protein, but instead generates noncoding RNA transcripts—many of which have no demonstrated function.

The human genome is filled with transcriptional noise and overlapping noncoding regions. The mere fact that a sequence is transcribed or bound by transcription factors does not confer functional necessity.

Even if the fusion site were repurposed as a weak promoter element (as some ENCODE data suggest), this co-option would have occurred long after the fusion, and does not negate the fusion's structural origin.

4. “The site binds transcription factors, so it's designed”

Tomkins points to data from the UCSC Genome Browser and the FANTOM project showing transcription factor binding and transcription start sites in the fusion region.

Rebuttal:

Transcription factor binding is not uncommon in repetitive or ancient regions of the genome and often reflects permissive or weak binding, not high-function promoters.

Binding alone doesn't prove functional regulation, especially without conserved enhancer/promoter architecture or knockdown/knockout evidence.

Many ancient or transposable-element-derived sequences acquire secondary roles or mild regulatory effects. This is expected in evolutionary genomics, not a mark of intelligent design.

The evolutionary co-option of a formerly structural element (the fusion site) into a regulatory context is an example of exaptation, a well-documented evolutionary phenomenon.

5. “There is no synteny around the fusion site”

Tomkins claims the surrounding region lacks synteny with the chimp genome, undermining the fusion hypothesis.

Rebuttal:

This is flatly incorrect. Numerous peer-reviewed genomic analyses show that the genes surrounding the fusion site in human chromosome 2 correspond in order and orientation to two separate chimpanzee chromosomes: 2p and 2q.

The discrepancy Tomkins notes likely stems from older chimp genome assemblies or from misalignment due to the high repetitive content in the region. Modern assemblies and comparative tools show clear syntenic alignment.

Furthermore, the centromere of human chromosome 2 corresponds to one of the two ancestral chimp centromeres, while a cryptic centromere remains as a fossil—supporting the fusion model.

6. “The cryptic centromere isn't valid”

Tomkins claims the so-called "fossil" centromere in chromosome 2 doesn't match human or ape centromeres in structure or alphoid DNA content.

Rebuttal:

Fossil centromeres, by definition, are degenerate and non-functional. We don't expect them to look like active centromeres. Their partial similarity and degraded state support the prediction that one ancestral centromere became inactive.

Alphoid DNA is highly variable across chromosomes and species, so lack of a perfect match between the fossil centromere and current centromeres is expected, not disconfirming.

The presence of two centromeric regions, one active and one degraded, is exactly what evolutionary theory predicts for a fusion of two chromosomes.

7. “The sequence is not unique—it occurs elsewhere”

Tomkins claims that telomere-like sequences are common throughout the genome, so the fusion site isn't special.

Rebuttal:

Telomere-like sequences (e.g., TTAGGG repeats) are found in scattered internal sites, but only one location in the genome contains:

• a head-to-head array of telomeric repeats,
• located in the exact position that would correspond to a fusion,
• flanked by sequences corresponding to two separate ape chromosomes,
• and accompanied by a cryptic centromere consistent with inactivation.

This unique convergence of features is not seen elsewhere and is far too specific to be dismissed as coincidence or random distribution.

Conclusion: Tomkins' Case Crumbles Under Scrutiny

Tomkins' arguments fail not because they raise novel concerns, but because they misrepresent or misunderstand the data. He shifts attention away from the robust structural features of the chromosome 2 fusion—head-to-head telomeric repeats, dual centromere remnants, and perfect synteny with chimp chromosomes—and instead fixates on superficial anomalies or reinterpretations of function.

Far from refuting fusion, Tomkins inadvertently confirms its reality by documenting how the site has been repurposed over time—a hallmark of evolutionary change, not divine engineering.

The human chromosome 2 fusion is not an artifact, illusion, or mistake. It is a genomic relic, a powerful confirmation of our shared ancestry with other great apes. That creationists like Tomkins must resort to such elaborate diversions to avoid its implications speaks volumes.

NOTES

[1] Jeffrey Tomkins, More DNA Evidence Against Human Chromosome Fusion, www.icr.org, July 31, 2015.