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The Ultimate Guide to Debunking Evolution’s “Best Evidence”
Why Common Design Explains the Data Better than Common Descent
by Donny Budinsky
Author’s Note
At Standing For Truth Ministries, we receive no shortage of critics. Over the years, we’ve engaged their challenges head-on—through books (including The Endogenous Retrovirus Handbook: Updated & Expanded), countless debates, lectures, and in-depth articles that carefully answer objections on every front of the origins debate. Those resources exist for readers who want detailed, comprehensive engagement with the best arguments evolutionists can offer.
This article has a different purpose.
Think of it as a cheat sheet—a quick-reference guide you can use in real-world conversations, Bible studies, or apologetics settings. It’s not here to anticipate every counter-rebuttal a critic might throw out. Instead, it’s designed to give concise, go-to responses to the most common “icons of evolution” you’ll encounter: homology, transitional fossils, chromosome 2 fusion, DNA similarity, and so on.
So if you’re looking for exhaustive detail, check out our other books, videos, and research publications. But if you need a practical, at-a-glance resource to pull out in discussion, this guide is for you.
Introduction
Evolutionists often claim the evidence for common ancestry is “overwhelming.” Textbooks, debates, and popular science outlets repeat the same arguments: homology, transitional fossils, chromosome 2 fusion, DNA similarity, and more. But when we examine the evidence carefully, we find that each piece is either agnostic (equally explainable by multiple models) or actually fits better within a creation framework.
This guide provides concise, go-to responses to the most common evidence for evolution. Use it as a reference in conversations, teaching, or personal study.
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Homology
Evolutionary claim: Shared structures across organisms point to inheritance from common ancestors.
Creation response: Human engineers design with homologous patterns. Cars from 3 different continents, such as those made from companies like GM, Toyota, and Volkswagen, all share four tires, windshields, and headlights—not because they evolved from a “common vehicle ancestor in the Arctic,” but because these are optimal design solutions. Biological homology likewise reflects common design, not common descent.
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Nested Hierarchies
Evolutionary claim: The tree-like classification of organisms supports descent with modification.
Creation response: Nested hierarchies also arise naturally in design systems. A sedan resembles a hatchback more than a van or a boat. Engineers don’t intentionally design in hierarchical patterns, but similarities naturally group into nested categories. Similarly, biological hierarchies reflect design logic. Importantly, such patterns enable advances in medicine and research—we rely on similarities between mice and humans, for example, to study disease.
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Transitional Fossils
Evolutionary claim: Transitional forms like Tiktaalik, the mammal-like reptiles, or Archaeopteryx demonstrate gradual evolution.
Creation response: The fossil record shows mosaics, not transitions. Archaeopteryx is fully bird with some reptile-like traits. Tiktaalik has both fish and tetrapod features. Likewise, engineers design crossover vehicles that blend both cars and vans, or military amphibious assault vehicles that combine boats and tanks. These are not “half-evolved” mistakes; they are purpose-built mosaics.
And remember: if evolution were true, there should be tens of thousands of unquestionable transitions, not a handful of disputed examples.
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Chromosome 2 Fusion
Evolutionary claim: Human chromosome 2 shows evidence of fusion, proving ancestry with chimps.
Creation response: Even if true, the fusion would have occurred in the human line—not showing relationship to chimps. Fusion fixation across all humanity is also problematic: how did a single uni-lateral mistake become universal in a global, scattered population?
Creation offers a cleaner solution: a post-Flood bottleneck could easily fix such a fusion within Noah’s family. Moreover, signatures resembling “fusion sites” appear elsewhere in the genome (e.g., chromosome 9) with no fusion history. Evidence is at best agnostic.
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Endogenous Retroviruses (ERVs)
Evolutionary claim: Shared ERVs are ancient viral scars inherited from common ancestors.
Creation response: ERVs are functional genetic elements. They regulate embryonic development (HERV-H), build immune protection in embryos (HERV-K), and even trigger anti-cancer viral mimicry through p53. Their resemblance to retroviruses is necessary for function—like an FBI agent infiltrating the mob must look the part.
ERVs fit far better as designed DNA units than as random viral leftovers. Shared sequences point to common design, not common descent.
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Pseudogenes
Evolutionary claim: Shared pseudogenes are broken genes inherited from common ancestors.
Creation response: Many pseudogenes are functional. They act as molecular decoys, regulate protein-coding counterparts, and control gene expression networks. The ENCODE project showed that at least 80% of the genome is biochemically active—far from useless junk.
Shared pseudogenes demonstrate shared design features that look similar because they serve similar purposes.
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Junk DNA
Evolutionary claim: Noncoding DNA proves evolutionary leftovers.
Creation response: Noncoding DNA is teeming with function—from regulatory RNAs to chromatin structure. If this activity were simply “noise,” as put forth by many defenders of common descent, natural selection should have eliminated wasteful transcription, since it consumes energy and ATP. Instead, widespread activity confirms the genome is economical and purposeful.
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Vestigial Organs
Evolutionary claim: Vestigial structures show leftover evolutionary baggage.
Creation response: Once, evolutionists listed over 100 vestigial organs. Today, virtually all have known functions. The appendix plays key roles in immunity. Whale “pelvic bones” anchor reproductive organs. These aren’t useless leftovers—they are functional features misinterpreted due to ignorance.
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DNA Similarity
Evolutionary claim: Humans and chimps share 98–99% of their DNA, proving common ancestry.
Creation response: That number is cherry-picked. When gaps, size differences, and structural variations are included, the figure drops to ~85% similarity (Nature, 2024). More importantly, similarity is agnostic—common design explains it just as well as common descent.
It’s the differences that matter: human and chimp Y chromosomes are <30% similar, with major structural differences and even missing arms (heterochromatin) in chimp DNA. Such massive differences are impossible to reconcile within evolutionary timeframes.
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Mutations and Natural Selection
Evolutionary claim: Beneficial mutations plus natural selection drive evolutionary progress.
Creation response: Mutations overwhelmingly break things—like rust on a car or typos in an encyclopedia. We inherit about 100 new mutations per person per generation. Most are slightly harmful; selection cannot remove them all. This leads to genetic degeneration, not innovation.
Even “beneficial” mutations are usually reductive (e.g., sickle-cell anemia protects against malaria but is caused by a broken hemoglobin protein). You don’t climb a mountain by falling more times than you step upward.
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Molecular Clocks
Evolutionary claim: Mutation rates show humans originated hundreds of thousands of years ago.
Creation response: Evolution relies on assumed slow rates. But observed pedigree-based rates are much faster: mtDNA mutation rates trace to a single mother only thousands of years ago (Biblical Eve), and Y chromosome rates trace to a single man about 4,500 years ago (Biblical Noah).
Observed data fits Biblical timelines—evolution stretches rates to fit deep time.
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Dating Methods
Evolutionary claim: Radiometric dating proves Earth is billions of years old.
Creation response: Dating methods are riddled with contradictions. Newly formed volcanic rocks often “date” as millions of years old. Different isotopes yield conflicting ages.
Meanwhile, short-lived C-14 is consistently found in “ancient” samples—coal, fossils, even diamonds—where none should remain after 100,000 years. Helium retention in zircon crystals also indicates a young Earth.
If the dating tools were reliable, such contradictions wouldn’t exist.
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Taxonomy
Evolutionary claim: Classification of organisms into kingdoms, families, and species reflects evolutionary history.
Creation response: Taxonomy is a human system of organization. We classify vehicles into sedans, SUVs, or trucks; we organize books by genre. That doesn’t mean sedans “evolved” into SUVs. Similarly, classifying animals doesn’t prove relationship—it’s just a useful tool for organization.
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Genetic Diversity
Evolutionary claim: The amount of DNA variation requires long evolutionary time.
Creation response: This assumes all diversity arose by mutations. Creationists instead argue for created heterozygosity—built-in DNA diversity from the start. Bottlenecks (Creation, Flood, Babel) reshaped but did not erase this diversity.
This explains why we see so much variation in humans and animals today without needing millions of years.
Conclusion
Every “best evidence” for evolution either collapses under scrutiny or is equally explained (therefore agnostic) by common design. When we step back, the picture is clear: the biological world is not the product of blind processes, but of brilliant design.
References
DNA Similarity & Y Chromosome
Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Cechová, M., Pál, K., … Phillippy, A. M. (2024).
The complete sequence and comparative analysis of ape sex chromosomes. Nature, 630(8016), 401–411. https://doi.org/10.1038/s41586-024-07473-2
Hughes, J. F., et al. (2012). Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature, 463(7280), 536–539. https://doi.org/10.1038/nature08700
Tomaszkiewicz, M., Medvedev, P., & Makova, K. D. (2017). Y and W chromosome assemblies: Approaches and discoveries. Trends in Genetics, 33(4), 266–282. https://doi.org/10.1016/j.tig.2017.01.008
Budinsky, D. (2025). Refuting Dr. Stefan Frello, Part One: The Y Chromosomes of Humans & Great Apes. Standing For Truth Ministries. https://standingfortruthministries.com/wp-content/uploads/2025/02/Refuting-Dr.-Stefan-Frello-Part-One-The-Y-Chromosomes-of-Humans-Great-Apes-1.pdf
Endogenous Retroviruses (ERVs)
Badarinarayan, S. S., & Sauter, D. (2021).
Switching sides: How endogenous retroviruses protect us from viral infections. Journal of Virology, 95(12), e02299-20. https://doi.org/10.1128/jvi.02299-20
Chuong, E. B., Elde, N. C., & Feschotte, C. (2017). Regulatory activities of transposable elements: From conflicts to benefits. Nature Reviews Genetics, 18(2), 71–86. https://doi.org/10.1038/nrg.2016.139
Grow, E. J., et al. (2015). Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature, 522, 221–225. https://doi.org/10.1038/nature14308
Budinsky, D. (2025). When ERVs Go Solo: Making Sense of Polymorphic LTRs in Humans and Mice. Standing For Truth Ministries.
Pseudogenes & Noncoding DNA
Poliseno, L., et al. (2010). A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465(7301), 1033–1038. https://doi.org/10.1038/nature09144
Pink, R. C., et al. (2011). Pseudogenes: Pseudo-functional or key regulators in health and disease? RNA, 17(5), 792–798. https://doi.org/10.1261/rna.2658311
ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74. https://doi.org/10.1038/nature11247
Mutations & Genetic Entropy
Sanford, J. C. (2014). Genetic entropy (4th ed.). FMS Publications.
Carter, R. W. (2019). Mendel’s Accountant: A biologically realistic forward-time population genetics program. In Sanford, J. et al. (Eds.), Biological Information: New Perspectives. World Scientific.
Radiometric Dating & Young Earth Evidence
Baumgardner, J. R. (2005). Carbon-14 evidence for a recent global flood and a young earth. In Vardiman, L., Snelling, A. A., & Chaffin, E. F. (Eds.), Radioisotopes and the Age of the Earth: Results of a Young-Earth Creationist Research Initiative (Vol. 2). Institute for Creation Research / Creation Research Society.
Humphreys, D. R. (2005). Helium diffusion age of zircons supports accelerated nuclear decay. In Vardiman, L., Snelling, A. A., & Chaffin, E. F. (Eds.), Radioisotopes and the Age of the Earth (Vol. 2).