Friday, 5 January 2024
Birds aren't little dinosaurs?
Fossil Friday: New Evidence Against Dinosaur Ancestry of Birds
This Fossil Friday we revisit the ancestry of birds, with the featured skeleton of the Late Cretaceous bird Hesperornis gracilis, exhibited at the Natural History Museum in Karlsruhe, Germany. Hesperornis was a flightless and toothed marine bird, somewhat similar to modern penguins, and lived contemporaneous with some of the raptor dinosaurs that are well known from the Jurassic Park movies.
Few hypotheses in evolutionary biology have become as popular among lay people as the postulated ancestry of birds from bipedal dinosaurs. Indeed, many a school kid will tell you proudly that birds simply are surviving dinosaurs. The theropod ancestry of birds has become an evolutionary dogma that is almost universally accepted and taught as the consensus view. However, there are a few dissenters, among whom the paleornithologist Alan Feduccia from the University of North Carolina certainly is the most prominent. He famously coined the term “temporal paradox” for the fact that the fossil record of the assumed theropod stem group of birds tends to be younger than the oldest actual birds. Last week I discussed new evidence that makes this temporal paradox much worse (Bechly 2023).
Beyond the Fossil Record
However, Feduccia’s critique of the dinosaur-bird hypothesis is not based just on problems with the fossil record, but also on conflicting evidence from comparative anatomy. Now, he presents new evidence that still more sharply contradicts the consensus view. One of the arguments for a dinosaur-bird relationship has been the presence of a so-called “open” acetabulum, which “is a concave pelvic surface formed by the ilium, ischium, and pubis, which accommodates the head of the femur in tetrapods.” Feduccia (2024) studied the acetabulum in early basal birds and found that their acetabulum tends to be partially closed and an antitrochanter (process of the ischium or iliac) is absent. This casts strongly into doubt one of the key characters for a dinosaur-bird relationship and suggests that this hypothesis must be re-evaluated. The fact that microraptorids and troodontids “also exhibit partial closure of the acetabulum and lack an antitrochanter is a further incongruity in that these taxa should exhibit “typical” theropod pelvic girdle modifications for terrestrial cursoriality.” This could support the view of several experts (e.g., Martin 2004, and various studies cited by Feduccia), that these maniraptoran taxa represent secondarily flightless birds rather than theropod dinosaurs.
Feduccia concluded his new study with this remarkable statement:
The hypothesis that birds are maniraptoran theropod dinosaurs, despite the certitude with which it is proclaimed, continues to suffer from unaddressed difficulties … Until problems like those discussed here — and many others that continue to be dismissed either by appeal to “consensus” or through overconfidence in the results of phylogenetic analysis of morphological data — have satisfactorily been resolved, skepticism toward the current consensus and continued investigation of alternative hypotheses are needful for the promotion of critical discourse in vertebrate phylogenetics and evolutionary biology.
Birds and dinosaurs may not represent arbitrary chunks of an evolutionary grade after all, but may instead represent distinct natural kinds. At the very least, the evidence seems to be much more ambiguous, weaker, and less convincing than most evolutionary biologists love to pretend.
The inability of chance and necessity to navigate the fitness landscape.
Trapdoors in the Fitness Landscape: Scientists Revive Worries About an Evolutionary Metaphor
Sewall Wright concocted one of those metaphors in science that lingers long past its “best by” date. In 1932, he coined the term “the fitness landscape.” He envisioned a mythical land of peaks and valleys, with the peaks indicating higher fitness, and valleys populated by evolving organisms starting out on their journeys toward progressively higher fitness levels. Impelled by the struggle for existence, organisms would climb higher till reaching a peak. One difficulty with this picture appeared soon after the metaphor gained popularity: to get to a higher peak, an organism would have to climb down, lowering its fitness on the way to a neighboring peak. Some workarounds 7were concocted, but the evocative metaphor lent itself to 3-D graphs and formulas of positive selection, giving evolutionary biologists hopes of empirical rigor as they measured their research organism’s progress up the landscape.
Stability of the Landscape
Unwarranted assumptions are the bugaboo of clever models like this. One is the stability of the landscape. Does the hypothetical landscape undulate over time, such that a peak at one epoch becomes a valley in another? After all, the dynamic environment is oblivious to the needs of organisms. How quickly does a given habitat change? How can evolutionists be sure that fitness for a savannah does not become a detriment if the population finds itself in a habitat undergoing desertification? For reasons like this, Mustonen and Lässig in 2009 dubbed it a fitness “seascape” instead of a landscape.
Another of Wright’s assumptions was that the fitness landscape follows Gaussian curves consisting of smooth lines without discontinuities. Even if some of those Gaussian curves rose steeply like a cliff, Darwin defenders like Richard Dawkins could get their organisms up to the summit of Mount Improbable by envisioning a gradual staircase from another direction, allowing natural selection to maintain Darwin’s narrative of the accumulation of small, incremental steps.
But what if the Gaussian assumption is wrong? What if, instead, the structure of the landscape is like a block of Swiss cheese, flat and riddled with holes that a blind watchmaker cannot foresee? The probability of a “holey” fitness landscape becomes credible when considering dependent traits. These “quantitative traits” are made up of components that must cooperate to work. Without all of them emerging simultaneously, no organism can ascend to higher levels. With dependent traits in operation, such as in the case of powered flight, a mutation or defect in one can send the organism to immediate extinction — as if, as in the old board game, a trapdoor opened underneath
This Is Not a New Worry
Sergey Gavrilets thought of this back in 1997 and raised it again in 2004. Now, worries about a “holey landscape” have been given new emphasis in a paper in PNAS — “Drift on holey landscapes as a dominant evolutionary process.” The four authors, from universities in North Dakota, California, and Paris, complain that this worry has been largely neglected.
Our understanding of selection has been strongly shaped by Sewall Wright’s conceptualization of an evolutionary landscape, with populations moving from areas of low fitness to areas of higher fitness. While the one- and two-trait landscapes Wright originally described have been criticized as unrealistic, including by Wright himself, the general metaphor has nonetheless guided much of evolutionary thought
What if the metaphor has “guided much of evolutionary thought” astray? Then, the “understanding of selection” has been shaped awry.
An important conclusion from this research is that evolutionary dynamics on simple landscapes often fail to properly predict evolution on higher dimensional landscapes. Empirical research into quantitative traits has been slow to incorporate this need for a higher-dimensional perspective.
Perhaps most conceptually unfamiliar and unintuitive to researchers focused on quantitative traits are holey landscapes (Fig. 1C; ref. 16). Holey landscapes are high-dimensional evolutionary landscapes that consist of trait combinations that are either of average fitness or that are inviable. This results in flat landscapes with holes at inviable or low fitness phenotypes (Fig. 1C)
Quantitative traits comprise “many aspects of physiology, behavior, and morphology,” they say, illustrating them with things like “most behaviors, physiological processes, and life-history traits.”
To investigate whether such traits tend to be distributed on a Gaussian landscape or a holey landscape, they looked at genetic variations in sixty species, including animals and plants. They found the results to be consistent with “high-dimensional, holey landscapes” instead of simplistic single-peak depictions or “badlands” landscapes consisting of rolling hills and gentle valleys. This suggested to them that
the leading conceptualizations and modeling of the evolution of trait integration fail to capture how phenotypes are shaped and that traits are integrated in a manner contrary to predictions of dominant evolutionary theory.Our results demonstrate that our understanding of how evolution has shaped phenotypes remains incompleteand these results provide a starting point for reassessing the relevance of existing evolutionary models.
Scrap and Start Over?
One way to reassess the relevance of an existing model is to scrap it and start over. The authors are not ready to try that, but they do point to serious shortcomings of conventional models: for instance, missing the holes.
Even more importantly, it is unknown what the topography of landscapes is for natural populations. While portions of selection surfaces and landscapes can be directly estimated, these estimates may differ from the full landscape due to several factors. These include the omission of fitness-affecting traits, incomplete estimation of fitness, and insufficient power to estimate non-linear selection coefficients.
In effect, modelers using Wright’s metaphor are building imaginary landscapes in thin air instead of working with real plants and animals on the real earth that must eat and survive. Simplistic Darwinian models of selection presuppose that beneficial mutations add up. This is not necessarily the case. A benefit to one gene can be a detriment to another — an example of negative pleiotropy. For realism, the whole animal must be considered, lest negative correlations open up a trapdoor that ends that organism’s progress, sending it down into one of those “inviable” outcomes. The authors call for better answers to the “crucial questions we have raised.”
Why would a holey landscape be flat? The authors explain what the model predicts for quantitative traits:
This topography stems from the multivariate nature of phenotypes: while there may be continuous fitness differences in two dimensions, fitness gradients will create holes in the landscape and peaks will average out when additional traits are considered. Unfortunately, predictions about quantitative trait evolution on holey landscapes are not clear and have rarely been pursued (e.g., ref. 18).
This means that traits are not isolated in one or two dimensions, but are interdependent on other traits in additional dimensions. This multi-dimensional consideration of traits on a flat landscape suggests that organisms are already at their optima; the fitness peaks have averaged out. The only way left is down, falling through a hole like a trapdoor if a trait changes that other traits depend on.
Irreducible Complexity and Devolution
The picture fits Michael Behe’s concepts of irreducible complexity and devolution. No part of a mousetrap should be considered in isolation. It may have a great spring, but if the other parts are weak or absent, the trap will not catch mice. Neo-Darwinism’s focus on positive selection of individual genes or traits, therefore, misses the holistic multi-dimensional view of organisms as functional wholes, to borrow Douglas Axe’s phrase. To function, a multi-dimensional trait must reach a threshold of coherence among its parts. These can be considered a list of design requirements.
Can neo-Darwinism recover from the neglected view of holey landscapes? The authors do not offer any hope, other than to wish that better landscape models may be forthcoming. Even with that concession, they remain pessimistic.
Our implementation of Wright’s metaphor represents only one of many possible evolutionary models. It is possible that unmodeled alternative landscapes may produce populations for which variation is distributed in a manner similar to holey landscapes and empirical estimates…. Importantly, and as mentioned previously, much of the exploration of evolution of quantitative traits has focused on simple landscapes like we have implemented here. Thus, it also is an open question what different models of selection “look” like when implemented for higher-dimensional phenotypes. For example, rugged landscapes of high dimensionality may give rise to holey landscapes as peaks average out and valleys are inviable…. Nonetheless, the close correspondence between empirical data and populations simulated as evolving on holey landscapes suggest that our understanding of quantitative trait evolution remains incomplete.
Regardless of any other possible devices to rescue the picture of progress up fitness peaks, they assert that “our finding that observed patterns of quantitative genetic variation across taxonomic groups are not consistent with traditional evolutionary models stands.”
This disconnect between observed patterns of multivariate variation and expectations under conventional models of selection suggests that Wright’s metaphor of landscapes — and the subsequent implementation of this metaphor as Gaussian surfaces — may have contributed to an incomplete understanding of how selection has shaped phenotypes. A potential contributor to this problem has been the lack of clear alternative explanationsbesides a simple null hypothesis of drift with no selection. Moving forward, clear development of additional alternative models of the action of selection and evolution in multivariate space is needed. This will allow the comparison of simulated populations to empirical data as we have done here.
Ultimately, our findings suggest that evolutionary biologists need to better consider the effects of high dimensionality as simple standard evolutionary models are not consistent with available data for quantitative data
Design Trumps Darwinism
Science is supposed to be about observable, quantitative data, isn’t it? If observations do not fit Wright’s convenient metaphor, the metaphor must be revised or discarded. Intelligent design is consistent with flat optima and built-in mechanisms to detect and avoid holes (e.g., DNA error correction, immune systems, blood clotting). Once again, design with its emphasis on engineering specifications trumps Darwinism in the real world.
Cicero echoes our brother Paul.
Cicero on Intelligent Design — Sound Familiar?
Yesterday was Cicero’s birthday. To celebrate, here’s my favorite quote from the Roman philosopher. From my Book Finding Truth: 5 Principles for Unmasking Atheism, Secularism, and Other God Substitutes:
“Yet we don’t really need the latest findings from science to recognize that a mind is needed to explain the universe. In every age, people have realized that an intelligible universe must be the product of intelligence.”
In ancient Rome, the Stoic philosophers offered an argument from design that sounds very familiar to modern ears. In the century before Christ, the great Roman orator Cicero wrote, “When we see something moved by machinery, like an orrery [model of the planetary system] or clock or many other such things, we do not doubt that these contrivances are the work of reason.”
He then drew the logical conclusion: “When therefore we behold the whole compass of the heaven moving with revolutions of marvelous velocity and … perfect regularity …, how can we doubt that all this is effected not merely by reason, but by a reason that is transcendent and divine?”
Sounding almost biblical in his language, Cicero wrote, “You see not the Deity, yet … by the contemplation of his works you are led to acknowledge a God.”
Clearly, people in the ancient world were capable of “reading” the message of general revelation in nature. The opening theme in Romans 1 is that anyone can conclude that the created order is the product of an intelligent being.
Ps.Romans Ch.1:20NIV"For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that people are without excuse."
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