Reality Corrects Evolutionary Tales, Part 1
Scientists rely on calibration for
accuracy, but sometimes the scientific
method itself needs to be calibrated
The Courage to Calibrate: When Reality Corrects the Story
By John D. Wise, PhD
Part 1. The Courage to Calibrate
Most scientific papers announce a new discovery, a new mechanism, or a new way to interpret data. Occasionally, however, scientists do something different. Instead of announcing a new discovery, they ask a more fundamental question:
How well are we doing science?
Our first paper is one of those, though you probably wouldn’t “get” that by the popular reportage:
Living alligators expose why juvenile fossils can fool classification methods, (Phys.org, 16 July 2026). This recent article in Phys.org summarizes new research by paleontologist James Napoli, a researcher at Stony Brook University’s Renaissance School of Medicine:
The challenge of correctly identifying a vertebrate fossil is that, as all creatures grow, their skeletons change dramatically. Young and adult animals often look so different that it is difficult to tell whether they are the same species, an issue long recognized by paleontologists. Additionally, without being able to witness a species grow or sequence its DNA, proper identification becomes even more uncertain. [emphasis mine].
The author proposes a way to reduce those mistakes and uncertainties by focusing on anatomical features that remain relatively constant throughout development. That’s the splashy announcement. However, the real core (and lasting importance, I believe) of this research is found in the details of the journal article:
Resolving the “ontogeny problem” in vertebrate paleontology (James G. Napoli, Paleobiology, 2 July 2026). In this research, Napoli is not merely proposing a minor refinement to a niche discipline. He is demonstrating one of the highest virtues of science: the courage to calibrate its methods against the reality science is supposed to be researching.
Measuring the Measuring Stick
Historical sciences face unique challenges. Unlike repeatable laboratory experiments in the present, they try to reconstruct unobservable events in the past. Whether the subject is paleontology, archaeology, or cosmology, researchers must infer past events from evidence in the present.
There is nothing inherently wrong with analysis aimed at reconstructive historical conjecture; every historical science depends upon it. But its practice begs a fundamental question: how do we know our reconstructive methods are trustworthy when we cannot travel back in time to check the results?
Noting this, Napoli’s experimental design is brilliantly simple.[1] Instead of testing paleontology’s standard inferential procedures on fragmentary fossils whose histories are unknown, he applies the field’s analytical tools to living crocodilians whose developmental and taxonomic histories are well understood in the present.
In other words, he chooses a case where reality can answer back in order to verify the methodological warrant for those in the past.
The Limits of the Digital Ruler
Paleontologists have for decades employed a technique known as Geometric Morphometrics (GM) along with a newer and more niche-method called cladistic analysis of ontogeny. These mathematical modeling tools treat ontogenetic change like evolutionary trees, promising to separate genuine species differences from the dramatic shapeshifting that naturally occurs as an animal grows from a juvenile to an adult.
But when Napoli applied these elegant computer models to living American and Chinese alligators, the methods shockingly failed to deliver on those promises.
Napoli reports:
“The failure of morphometric methods to recover obviously distinct groups in morphospace suggests that GM cannot effectively discriminate between anatomically similar species, especially when faced with ontogenetic and polymorphic variation within both… In sum, GM fails to empirically recover the known taxonomy of the trial dataset.”
Furthermore, he notes that the cladistic analysis of ontogeny failed to accurately describe the sequence of character changes in four out of five analytical trials. Of the single trial that technically “succeeded,” Napoli called it a “fluke” arising from ideal, a priori conditions, conditions physically impossible to obtain in true paleontological research.
The Circularity of ‘Baked-In’ Assumptions
Why do these sophisticated and – and widely trusted – scientific methods struggle? Napoli exposes a subtle assumption of circular reasoning. To make the mathematics work, evolutionary modelers frequently construct what they call an “artificial embryo,” a hypothetical, composite ancestor assembled from selected character states rather than direct observation, which is unavailable for nearly all extinct fossil species.
Additionally, because the smallest fossil specimens are commonly assumed to represent the earliest developmental stages before the software even runs, the procedure naturally “discovers” the exact evolutionary trajectory that the initial assumptions favored.
These procedures are promoted as objective tools that can reconstruct the past without human bias, but Napoli revealed a closed loop of circular reasoning. The story was already ‘baked in’ to the dataset before the analysis began. More regrettably, when the method fails, it does not just produce harmless statistical noise; it manufactures false evolutionary trends that radiate across the discipline, like claims regarding the “tendency toward a loss of tooth positions” – he says:
No clade shows a tendency toward a loss of tooth positions, despite published claims to the contrary.
If these procedures are not empirically testable – or tested, as Napoli does here, what level of confidence should science be placing in their results?
A Lesson Beyond Paleontology
The two living alligator species have supposedly spent 50 million years evolving along separate paths, giving them ample opportunity to lock in distinct physical traits. Yet when put to the test, paleontology’s premier software tools failed to separate them. If a method stumbles when faced with two living species separated by tens of millions of years of history, on what grounds should we trust it to decipher the subtle nuances of an incomplete fossil record?
Napoli has reminded us of a fundamental truth: before we trust a historical reconstruction, we must calibrate the reconstructive engines. Have we? Science progresses not by crowning the most elegant narrative, but by submitting its tools and methods to the uncompromising judgment of empirical reality. It is time for historical biology to stop celebrating its computer-generated stories, and start calibrating its storytellers.
Tomorrow: Another example of interpretation vs reality, in Part 2.
[1] I must admit that my admiration for and understanding of this methodology is deeply tempered by C S Lewis’s brilliant “takedown” of biblical Higher Criticism in his article, “Modern Theology and Biblical Criticism” in Christian Reflections, Eerdman’s, 1967. I highly recommend it if you haven’t read it.
John Wise received his PhD in philosophy from the University of CA, Irvine in 2004. His dissertation was titled Sartre’s Phenomenological Ontology and the German Idealist Tradition. His area of specialization is 19th to early 20th century continental philosophy.
He tells the story of his 25-year odyssey from atheism to Christianity in the book, Through the Looking Glass: The Imploding of an Atheist Professor’s Worldview (available on Amazon). Since his return to Christ, his research interests include developing a Christian (YEC) philosophy of science and the integration of all human knowledge with God’s word.
He has taught philosophy for the University of CA, Irvine, East Stroudsburg University of PA, Grand Canyon University, American Intercontinental University, and Ashford University. He currently teaches online for the University of Arizona, Global Campus, and is a member of the Heterodox Academy. He and his wife Jenny are known online as The Christian Atheist with a podcast of that name, in addition to a YouTube channel: John and Jenny Wise.