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The Positive Case for Intelligent Design in Systematics (the Relationships Between Organisms)

Photo: Mexican free-tailed bats, by dizfunkshinal, CC BY 2.0 , via Wikimedia Commons.

Editor’s note: We are delighted to present a series by geologist Casey Luskin on “The Positive Case for Intelligent Design.” This is the fifth entry in the series, a modified excerpt from the new book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the CosmosFind the full series so far here.

Observation (from previous studies): Intelligent agents reuse functional components in different systems (e.g., wheels for cars and airplanes, or keyboards on cell phones and computers): 

  • “An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently.”1
  • “According to this [evolutionary] argument, the Darwinian principle of common ancestry predicts such common features, vindicating the theory of evolution. One problem with this line of argument is that people recognized common features long before Darwin, and they attributed them to common design. Just as we find certain features cropping up again and again in the realm of human technology (e.g., wheels and axles on wagons, buggies and cars), so too we can expect an intelligent designer to reuse good design ideas in a variety of situations where they work.”2
  • “[I]f different forms of life were intelligently designed, with a mosaic of characteristics, some of which they share in common with some organisms and others of which they share in common with different organisms, then we would expect ‘phylogenetic’ analyses to generate conflicting trees depending on which character was chosen. Indeed, phylogenetic analyses of different characters present in several different human-designed technological objects have been shown to generate precisely such conflicting trees.”3

Hypothesis (prediction): Genes and other functional parts will be reused in different and unrelated organisms in a pattern that need not match a “tree,” or nested hierarchy.

Experiment (data): Similar parts have been found reused in widely different organisms where even evolutionists believe the common ancestor did not have the part in question. Examples include similar genes controlling eye or limb growth in different organisms whose alleged common ancestors are not thought to have had such forms of eyes or limbs.4 There are numerous examples of extreme convergent genetic evolution, including similar genes used in whales and bats for echolocation.5 Genes and functional parts are frequently not distributed in a “treelike” pattern or nested hierarchy predicted by common ancestry, but rather, show reusage in a non-nested pattern.6 One mainstream scientific paper acknowledges:

Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species…phylogenetic conflict is common, and frequently the norm rather than the exception.7

Conclusion: Common design is prevalent throughout life. The re-usage of highly similar and complex parts in widely different organisms in non-treelike patterns is best explained by the action of an intelligent agent.

Next, “The Positive Case for Design in Genetics”


  1. Paul Nelson and Jonathan Wells, “Homology in Biology,” Darwinism, Design, and Public Education, 303-322.
  2. William A. Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy (Downers Grove, IL: InterVarsity, 2010), 85.
  3. Günter Bechly and Stephen C. Meyer, “The Fossil Record and Universal Common Ancestry,” Theistic Evolution: A Scientific, Philosophical, and Theological Critique, eds. J.P. Moreland, Stephen C. Meyer, Christopher Shaw, Ann K. Gauger, and Wayne Grudem (Wheaton, IL: Crossway, 2017), 331-361.
  4. R. Quiring et al., “Homology of the eyeless gene of Drosophila to the Small eye in mice and Aniridia in humans,” Science 265 (August 5, 1994), 785-789; D.B. Wake et al., “Homoplasy: from detecting pattern to determining process and mechanism of evolution,” Science 331 (February 25, 2011), 1032-1035.
  5. P.-A. Christin et al., “Causes and evolutionary significance of genetic convergence,” Trends in Genetics 26 (2010), 400-405; Y. Li et al., “The hearing gene Prestin unites echolocating bats and whales,” Current Biology 20 (January 2010), R55-R56; G. Jones, “Molecular Evolution: Gene Convergence in Echolocating Mammals,” Current Biology 20 (January 2010), R62-R64.
  6. For example, see W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science 284 (June 25, 1999), 2124-2128; W. Ford Doolittle, “Uprooting the Tree of Life,” Scientific American (February 2000), 90-95; Arcady R. Mushegian et al., “Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes,” Genome Research 8 (1998), 590-598; James H. Degnan and Noah A. Rosenberg, “Gene Tree Discordance, Phylogenetic Inference and the Multispecies Coalescent,” Trends in Ecology and Evolution 24 (2009), 332-340; Eric Bapteste et al., “Networks: Expanding Evolutionary Thinking,” Trends in Genetics 29 (August 2013), 439-441; Graham Lawton, “Why Darwin Was Wrong about the Tree of Life,” New Scientist (January 21, 2009), 34-39; Trisha Gura, “Bones, Molecules, or Both?” Nature 406 (July 20, 2000), 230-233; Anna Marie A. Aguinaldo et al., “Evidence for a Clade of Nematodes, Arthropods, and Other Moulting Animals,” Nature 387 (May 29, 1997), 489-493; Erich D. Jarvis et al., “Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds,” Science 346 (December 12, 2014), 1320-1331; Ewen Callaway, “Flock of Geneticists Redraws Bird Family Tree,” Nature 516 (December 11, 2014), 297; Emma C. Teeling and S. Blair Hedges, “Making the Impossible Possible: Rooting the Tree of Placental Mammals,” Molecular Biology and Evolution (2013); James E. Tarver et al., “The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference,” Genome Biology and Evolution 8 (2006), 330-344; Jeffrey H. Schwartz and Bruno Maresca, “Do Molecular Clocks Run at All? A Critique of Molecular Systematics,” Biological Theory 1 (December 2006), 357-371; Maximilian J. Telford, “Fighting Over a Comb,” Nature 529 (January 21, 2016), 286; Antonis Rokas; “My Oldest Sister Is a Sea Walnut?” Science 342 (December 13, 2013), 1327-1329; Benjamin J. Liebeskind et al., “Complex Homology and the Evolution of Nervous Systems,” Trends in Ecology and Evolution 31 (February 2016), 127-135; Amy Maxmen, “Evolution: You’re Drunk: DNA Studies Topple the Ladder of Complexity,” Nautilus 9 (January 30, 2014), http://nautil.us/issue/9/time/evolution-youre-drunk (accessed October 28, 2020); David A. Legg et al., “Cambrian Bivalved Arthropod Reveals Origin of Arthrodization,” Proceedings of the Royal Society B 279 (2012), 4699-4704; Mark S. Springer et al., “Endemic African Mammals Shake the Phylogenetic Tree,” Nature 388 (July 3, 1997), 61-64; William J. Murphy et al., “Molecular Phylogenetics and the Origins of Placental Mammals,” Nature 409 (February 1, 2001), 614-618; F. Keith Barker et al., “Phylogeny and Diversification of the Largest Avian Radiation,” Proceedings of the National Academy of Sciences USA 101 (July 27, 2004), 11040-11045; Rodolphe Tabuce et al., “Early Tertiary Mammals from North Africa Reinforce the Molecular Afrotheria Clade,” Proceedings of the Royal Society B 274 (2007), 1159-1166.
  7. Liliana M. Dávalos et al., “Understanding phylogenetic incongruence: lessons from phyllostomid bats,” Biological Reviews of the Cambridge Philosophical Society 87 (2012), 991-1024.