F Rosa Rubicondior: Creationism in Crisis - How The Fossil Record Provides Evidence For Evolution - No Magic Needed

Friday 16 February 2024

Creationism in Crisis - How The Fossil Record Provides Evidence For Evolution - No Magic Needed

Desert sand dune landscape of the Upper Cretaceous Djadokhta/Baruungoyot Formations. Foreground: the large-bodied monstersaurian lizard Estesia mongoliensis predating on the enantiornithine bird Gobipteryx minuta.

Illustration by Nathan Dehaut
A Lighthouse in the Gobi Desert | Natural History Museums of Los Angeles County

We are regularly told by creationists who have either been fooled by a lie, or are trying to fool us with one, that biomedical scientists are increasingly rejecting the Theory of Evolution and replacing it with the notion of intelligent design.

This was, of course, the aim of the Discovery Institute's 26-year-old, 5-year[sic] strategy detailed in The Wedge to insert Bible literalism into mainstream science, apparently believing that for the first time in the history of science, a well-established scientific theory is going to be replaced by a an evidence-free superstition based on misrepresentation of the data and including unproven supernatural entities doing magic.

Intelligent design creationism, of course, doesn't meet the basic criteria to be called a science, which is why any scrutiny of the relevant scientific literature will find no hint that the TOE is inadequate for explaining the data or that magic explains it in a more scientifically satisfying way. Indeed, as I repeatedly show in these blog-posts, virtually every piece of scientific research casually refutes creationism by revealing the evidence and not a single peer-reviewed biomedical science paper ever concludes that intelligent design is the only way to explain the observations.

As Michael J Behe was forced to admit in the Kitzmiller case, "There are no peer-reviewed article by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred". And that situation has not changed since Behe effectively sank the Wedge Strategy with that grudging admission under oath in an American court. Instead, we find papers like this technical one in which a team of researchers led by Dr. Hank Woolley, a Postdoctoral Research Fellow at the Dinosaur Institute, Natural History Museum of Los Angeles County, and the Department of Earth Sciences, University of Southern California, Los Angeles, California, discuss and evaluate the degree to which exceptional collections of fossils, such as those found in the Gobi Desert of Central Asia can influence our understanding of evolutionary relationships between fossil groups - what they term the lagerstätten effect .

The team have explained their research in a news release from the Natural History Museums of Los Angeles County:
A Lighthouse in the Gobi Desert

A new study quantifies the impact of the world’s great fossil sites on our understanding of evolutionary relationships between fossil groups and discovers the key to understanding lizard evolutionary history in the Gobi Desert.

A new study published in the journal PLoS ONE explores the weight great fossil sites have on our understanding of evolutionary relationships between fossil groups—the lagerstätten effect—and for the first time, quantified the power these sites have on our understanding of evolutionary history. Surprisingly, the authors discovered that the wind-swept sand deposits of the Late Cretaceous Gobi Desert’s extraordinarily diverse and well-preserved fossil lizard record shapes our understanding of their evolutionary history more than any other site on the planet.

While famous as the region where Velociraptor was discovered, China and Mongolia’s Late Cretaceous Gobi Desert might have more of an impact on our understanding of ancient—and modern—life thanks to its rich record of fossil lizards.

What's so cool about these Late Cretaceous Gobi Desert deposits is that you're getting extremely diverse, exceptionally complete, three-dimensionally-preserved lizard skeletons. You're getting many lineages on the squamate Tree of Life represented from this single unit, giving us this remarkable fossil signal of biodiversity in the rock record, something that stands out as a lighthouse in the deep dark chasms of squamate evolutionary history.

Where there’s exceptional preservation—hundreds of species from one part of the world at one period of very specific time—that doesn't necessarily give you a good idea of global signals. It's putting its thumb on the scale.

Dr. C. Henrik (Hank) Woolley, lead author
Dinosaur Institute
Natural History Museum of Los Angeles County
Los Angeles, California, USA
And the Department of Earth Sciences
University of Southern California
Los Angeles, California, USA
More complete skeletons make it easier to trace relationships through time by making it easier to compare similarities and differences. The more complete a skeleton is, the more traits are preserved, and those traits translate into phylogenetic data—data that are used to construct the tree of life.

To measure how impactful deposits of exceptional fossil preservation (known in the paleontology community by the German term “lagerstätten”) are on the broader understanding of evolutionary relationships through time, Woolley and co-authors including Dr. Nathan Smith, Curator of the Dinosaur Institute, combed through published records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (the group of reptiles that includes mosasaurs, snakes, and lizards).

The Fossil Meta Narrative

When it came to squamates, the researchers found no correlation between the intensity of sampling and whether any given site impacted phylogenetic data on a global scale. Instead, they found a signal from depositional environments, the different kinds of sites where sediments accumulated, preserved markedly different groups.

Because the squamate record from the Gobi Desert is so complete, it shapes our understanding of squamate evolution around the world and across time, a prime example of the “lagerstätten effect”—despite not being a typical lagerstätte. Traditional lagerstätten deposits come from marine chalks, salty lagoons, and ancient lake environments—not from arid sand dunes. The ancient environment shapes what gets preserved in the fossil record.

We were not expecting to find this detailed record from lizards in a desert sand dune deposit.

Dr. C. Henrik (Hank) Woolley

We often think of lagerstätten deposits as preserving soft tissues and organisms that rarely fossilize, or especially rich concentrations of fossils. What makes the Gobi squamate record unique, is that it includes both exceptionally complete skeletons, and a high diversity of species from across the group’s family tree.

Dr. Nathan Smith, co-author
Curator Dinosaur Institute
Natural History Museum of Los Angeles County
Los Angeles, California, USA.
Graphical summary of the results of the new study. A) Summary of the phylogenetic impact of the Late Cretaceous Gobi Desert lizard assemblage. B) Comparison to other well-preserved squamates found in lake deposits.

We're at this frontier between fields within paleontology that rarely overlap: assessing evolutionary relationships of fossil groups (phylogenetics) and assessing how things fossilize (taphonomy). Exploring this frontier will help to incorporate more of Earth’s extinct biodiversity in museum collections as we piece together the past.

Dr. C. Henrik (Hank) Woolley
More technical detail and background is given in the abstract and introduction to the team's paper in PLOS ONE:

Fossil deposits with exceptional preservation (“lagerstätten”) provide important details not typically preserved in the fossil record, such that they hold an outsized influence on our understanding of biodiversity and evolution. In particular, the potential bias imparted by this so-called “lagerstätten effect” remains a critical, but underexplored aspect of reconstructing evolutionary relationships. Here, we quantify the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards, snakes, mosasaurs), and then compare the influence of lagerstätten deposits on phylogenetic information content and taxon selection in phylogenetic analyses to other fossil-bearing deposits. We find that groups that preserve a high amount of phylogenetic information in their global fossil record (e.g., non-avian theropods) are less vulnerable to a “lagerstätten effect” that leads to disproportionate representation of fossil taxa from one geologic unit in an evolutionary tree. Additionally, for each taxonomic group, we find comparable amounts of phylogenetic information in lagerstätten deposits, even though corresponding morphological character datasets vary greatly. Finally, we unexpectedly find that ancient sand dune deposits of the Late Cretaceous Gobi Desert of Mongolia and China exert an anomalously large influence on the phylogenetic information available in the squamate fossil record, suggesting a “lagerstätten effect” can be present in units not traditionally considered lagerstätten. These results offer a phylogenetics-based lens through which to examine the effects of exceptional fossil preservation on biological patterns through time and space, and invites further quantification of evolutionary information in the rock record.


Any effort to reconstruct biodiversity in Earth’s geologic past hinges on the ability to characterize and quantify the downstream effects of bias in the fossil record. Fossil data, from a cellular to a global level, is subject to various geological filters [1, 2], taphonomic filters [3], and sampling filters [4, 5], that distort our understanding of ancient life. If left unaccounted for, these biases represent significant barriers to paleobiological inquiry [6] that can obscure the myriad of anatomical, ecological, and evolutionary signals contained in the rock record.

Although the incompleteness of fossil data is a long-established reality in paleobiology [58], a growing number of studies have employed a variety of novel metrics to characterize and quantify fossil record biases in organismal groups [924]. Combined with an increasing number of sampling proxies to account for a multitude of biases in paleobiological data [22, 2527], we are equipped with an advanced toolkit to explore outstanding questions related to biodiversity in the fossil record. However, the association between fossil record incompleteness and our ability to infer evolutionary relationships of fossil organisms remains a pressing, but underexplored question [3, 2831].

Using established “completeness metrics” for a fossil record is one of the most straightforward ways to assess potential barriers to reconstructing the phylogeny of extinct organisms. In this study, we use the Character Completeness Metric (CCM [10]), to measure the percentage of phylogenetic characters that can be scored for a given fossil species, based on the preserved elements of a species’ anatomy. The CCM is extremely useful in quantifying both the physical completeness of the fossil record of organismal groups, but also quantifies potential barriers to accurately reconstructing their evolutionary relationships, which are essential to the frameworks that synthetic studies of biodiversity [32], biostratigraphy [33], and paleobiogeography [34] rely upon. Here, we use the CCM to quantify the amount of phylogenetic information available in the global fossil records of three prominent tetrapod groups: non-avian theropod dinosaurs (defined here as all theropods excluding Avialae [20]), Mesozoic birds (defined here as all Mesozoic taxa included in Avialae [11]), and squamates (e.g., lizards, snakes, amphisbaenians, and mosasaurs). The biases we set out to quantify in detail are 1) the relationship between regional sampling intensity and amount of phylogenetic information preserved; 2) the relationship between depositional environment and amount of phylogenetic information preserved.

The approach in this study allows us to quantify which depositional settings are more likely to preserve higher amounts of phylogenetic information, and which landmasses have historically produced the highest amount of phylogenetic information. In examining these two biases, we can also quantitatively visualize novel patterns in the preservation of phylogenetic data in the fossil record. Specifically, we highlight an unexpected finding: the lizard assemblage from the Upper Cretaceous aeolian deposits of the Gobi Desert (Djadokhta and Baruungoyot Formations [3540]) preserves an extremely high amount of phylogenetic information compared to all other geologic units in the squamate fossil record, including diverse squamate assemblages found in established “lagerstätten” deposits (e.g., Solnhofen [4144], Jehol [4547], Messel, [4853], Quercy Phosphorites [51, 5457]).

“Lagerstätten” [5860] are unusually rare confluences of deposition, taphonomy, and diagenesis that produce exceptionally preserved fossil assemblages. Lagerstätten are found across billions of years of geologic time [61] and include some of the most famous and intensely-studied fossil assemblages on the planet [6266]. The biological information we gain from rare lagerstätten deposits often substantially exceeds what is preserved in the vast majority of “normal” fossil deposits, and as such have been identified as having an anomalous impact on studies of ecology, diversification and extinction through time [4, 6, 59, 61, 67]. Commonly referred to as the “lagerstätten effect”, the outsized influence that rare exceptionally preserved deposits have on the understanding of evolution through time can be at once a paleobiological boon to researchers [61] and a major source of bias in our understanding of the morphological evolution of a given group or groups of organisms [4, 6, 67]. The “lagerstätten effect” is famously acute in reconstructing global biodiversity changes through geologic time [6, 67, 68]. Lagerstätten often preserve such anomalously high amounts of fossil species relative to typical “baseline” sedimentary processes that estimations of global fossil diversity and abundance are more accurate when removing them from the dataset [61, 67]. This paradoxical bias has other important downstream impacts in analyzing biological and evolutionary patterns in Earth’s past. In particular, when it comes to inferring the phylogenetic relationships of organismal groups using their fossil record, the “lagerstätten effect” on phylogenetic information content and incorporation of taxa into analyses remains underexplored, and needs to be characterized to avoid bias in evolutionary interpretations [34, 6, 2829, 67].

The pattern this study describes in the squamate fossil record invites us to consider whether deposits that lack traditional lagerstätten features (soft-bodied preservation, extreme abundance, etc.), such as the Djadokhta and Baruungoyot Formations in the Late Cretaceous Gobi Desert [3540], can still have lagerstätten-level preservation of evolutionary information. These units could thus impart a phylogenetic “lagerstätten effect” [67] that overloads phylogenetic analyses with taxa from one geographic area or timeframe, potentially biasing estimates of important aspects of evolutionary history, such as biogeography [34] and lineage divergence times [6]. We find that the effect that the Djadokhta and Barrungoyot Formations have over the quality of the fossil record of squamates is similar to the well-established “lagerstätten effect” due to the exceptionally high amount of phylogenetic information in Mesozoic birds from the Jehol Biota on our understanding of avialan evolution [11, 68]. Non-avian theropods are well-represented in both the Late Cretaceous Gobi and Jehol Biota, but have a much more complete global fossil record than either squamates or Mesozoic birds, and thus are not as vulnerable to a “lagerstätten effect” on their phylogenetic history. These results offer a novel lens through which to examine the effects of exceptional preservation on phylogenetic information content in fossil groups.
Fig 1. Visualization of the Character Completeness Metric (CCM2) in the fossil record of non-avian theropod dinosaurs, Mesozoic birds, and squamates.

A) Heat map of non-avian theropod phylogenetic character density across the skeleton of an example theropod, Teratophoneus curriei, [71] on public display at the Natural History Museum of Utah. B) Heat map of avian phylogenetic character density across the skeleton of an example Mesozoic bird, Archaeopteryx lithographica [72], on public display at the Natural History Museum of Los Angeles County. C) Heat map of character density across an example squamate skeleton (Uta stansburiana). D) Summary violin plots for the phylogenetic completeness (CCM2) of described species in the global fossil record of non-avian theropods (top), Mesozoic birds (middle) and squamates (bottom). White dot: median; black bar: interquartile range; black line: 95% confidence interval. Silhouettes traced from publicly-available renderings at www.phylopic.org.
There is, of course, no hint of doubt that the evidence of the fossil record is the basis for estimating evolutionary relationships between phylogenies; the debate is about how to ensure the evidence is not unduly weighted by the abundance of that evidence in these lagerstätten and so failing to include data from less plentiful sites so ending up with a local phylogeny rather than reflecting global evolutionary changes.

But creationists who know their claims are false will misrepresent papers like this as evidence that scientists have discovered flaws in the techniques or proven that the currently accepted evolutionary relationships might be wrong, and expect their dupes to believe that this is evidence that biologists are discovering the TOE to be wrong.

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