Monday, April 8, 2024

How science is - and should not be - done

 Fossil Friday: New Study Confirms “Feathered Dinosaurs” Were Secondarily Flightless Birds

Günter Bechly

April 5a Commons.

This Fossil Friday features one of the most well-known fossils of all, the famous Berlin specimen of the ancient bird Archaeopteryx from the Late Jurassic Solnhofen lithographic limestone in Bavaria. This iconic fossil was often considered to be a missing link between dinosaurs and birds, and thus a poster-child for fossil evidence in favor of Darwinian evolution.

In several past articles at Evolution News I have discussed the work of paleo-ornithologist Alan Feduccia, who courageously challenged the current consensus view that birds evolved from dinosaurs, as first suggested by Yale paleontologist John Ostrom in the mid 1970s with his Birds-are-Maniraptoran-Theropods (BMT) hypothesis. Feduccia elaborated his opposing views in numerous technical articles and four popular books titled “The Age of Birds“ (Feduccia 1980), “The Origin and Evolution of Birds” (Feduccia 1996), “Riddle of the Feathered Dragons” (Feduccia 2012), and most recently “Romancing the Birds and Dinosaurs” (Feduccia 2020). In a highly recommended review of the latter book, James (2021) wrote that “Every school child knows that birds are dinosaurs. Numerous magazine articles and popular books on the topic are available,” which is a remarkable success of selling a relatively recent scientific hypothesis to a wide general audience as an established fact. James continues that “in spite of all this confidence that the problem of the origin of birds has been solved, strong grounds exist for regarding the issue as unsettled, … Surely, admitting that the hypothesis that birds are maniraptoran theropods has serious problems would be better than to defend it so strongly.”

Three General Objections

In a review of Feduccia’s earlier book on the “Riddle of the Feathered Dragons,” Leigh (2014) listed three general objections by Feduccia to Ostrom’s dinosaur-to-bird hypothesis:

1.   Most of the fossils used to support the theropod ancestry of birds are 20 million or more years younger than Archaeopteryx [this was famously labeled by Feduccia as a “temporal paradox”].

2.   Theropod dinosaurs, Deinonychus included, were runners. It is much more reasonable to believe that, like bats and pterosaurs, birds descended from arboreal animals that evolved flight via the ability to glide.

3.   The fossil record suggests that feathers evolved in connection with gliding and flying, rather than as insulation, or as part of an apparatus for catching insects, as Ostrom had suggested.

James (2021) listed several further problems that Feduccia has identified in his most recent book, which support his alternative view:

·         Neoflightless problem: Some flying and flightless birds are being misclassified as theropods.

·         Data analysis problem: Standard phylogenetic analyses are unable to detect complex evolutionary processes like convergence. Flightless birds converge on the body plan of theropods. To estimate basic similarities (homologies), anatomical studies are needed before the phylogenetic analysis.

·         Reduced forelimb problem: Complex characters, once lost, are unlikely to reevolve. Dollo’s Principle.

·         Protofeather problem: “Protofeathers” may be degraded collagen fibers.

·         Digit problem: The frame shift is a verificationist explanation, designed to fit the BMT.

·         Behavior problem: Studies that infer bird-like behavior in dinosaurs are about misidentified birds.

·         Confirmation problem: Scansoriopterygids have no distinctive theropod characters. An assumption that they are theropods is a form of confirmation bias. 

Geist (2022) commented in his review of the same book:

Feduccia leads readers through case after case where scientists, to accommodate the cladograms supporting the BMT hypothesis, have gone to extraordinary lengths to work around data that directly contradict their conclusions. Such efforts violate another bedrock, though not ironclad, philosophy of science: Occam’s Razor, stating that given multiple hypotheses, the simplest of competing theories be preferred over the more complex. Feduccia elegantly illustrates cases where conclusions drawn from cladistic analysis that dictate the connection between birds and dinosaurs violate this principle. At the very least this book might convince supporters of BMT to reevaluate the data.

This failure of cladistics was admitted by John Ostrom (1994: 172) himself, who commented that “reasoning of such dubious quality demonstrates a fundamental flaw in cladistic methodology. Preoccupation with compilation of lengthy lists of shared derived characteristics at the expense of a well-reasoned analysis will result in an erroneous phylogeny every time.”

Responding to Feduccia

So, how did the proponents of the dinosaurian ancestry of birds respond to Feduccia’s profound challenges? They did as Darwinists always do when their pet hypotheses are challenged with actual data: they ridicule and marginalize the critique or reduce it to a straw-man caricature. Here is what Ruben (1997) wrote in his review of Feduccia’s second book:

Specialists who are concerned with avian origins, especially those advocating a dinosaur-bird lineage, will be forced to confront a variety of previously ignored data that argue against this lineage. Thus, it hardly comes as a surprise that the book has been dismissed in recent reviews by several particularly zealous, cladistically oriented paleontologists. However, readers should not be misled by such shenanigans.

Zealous shenanigans? This is quite revealing for an alleged unbiased quest for scientific truth.

The Neoflightless Hypothesis

But, how does Feduccia explain the indisputable great similarity between vane-feathered bipedal dinosaurs (called Pennaraptora) and true birds? Actually, he does not dispute a close relationship at all, but suggests that Pennaraptora were not theropod dinosaurs but rather secondarily flightless birds, which he called the neoflightless hypothesis. Incidentally, the same claim has been made by skeptics of Darwinian evolution.

Now, a new study by Kiat & O’Connor (2024) published in the Proceedings of the National Academy of Sciences provides strong additional support to the neoflightless hypothesis (also see the press releases by Field Museum 2024 and Koumoundouros 2024). The scientists studied the wing feathers in hundreds of different living bird species of all major orders, and detected a simple pattern that reliably distinguishes secondarily flightless birds from those that can fly: the latter always have 9-11 asymmetrical flight feathers called primaries, while the former have either significantly more or none at all. Furthermore, the degree of primary vane asymmetry turned out to be strongly related to flight. This allowed the researchers to look at 65 species of fossil birds and feathered dinosaurs to estimate their ability to fly. Unsurprisingly, Archaeopteryx and the four-winged Microraptor passed the litmus test for flight.

Much more surprisingly, the study suggests that feathered dinosaurs like “Caudipteryx possessed the correct number of primary feathers but they were almost completely symmetrical, ‘almost certainly’ ruling out flight” (Koumoundouros 2024). The authors concluded that “applying these data to extinct pennaraptorans suggests that anchiornithines and the oviraptorosaur Caudipteryx are secondarily flightless. The phylogenetic position of these species suggests that volant abilities are plesiomorphic to Pennaraptora.” In other words, all those feathered dinosaurs originally had wings like birds and could fly, and thus do not represent transitional stages in the evolution of avian flight from cursorial dinosaurs. They are no help at all to explain the origin of pennaceous feathers and wings. This also makes very recent studies obsolete, which proposed scenarios to derive the bird wing from more primitive structures in maniraptoran dinosaurs, such as the propatagium in Caudipteryx and Microraptor (Uno & Hirasawa 2023, also see University of Tokyo 2023). As new data accumulate at an ever faster rate, the shelf life of evolutionary story telling is plummeting from decades to only months.

Trust the Science?

Should you really just trust the science (but not too long)? Alan Feduccia can rightfully claim an important empirical confirmation of his theory, and Darwinists may have to say goodbye to some cherished assumed transitional forms and the evolutionary just-so stories built upon them. But there is more: Kiat & O’Connor (2024) explicitly admit that “the results of these analyses support a single origin of dinosaurian flight and indicate the early stages of feathered wing evolution are not sampled by the currently available fossil record.” It looks very much like flying vertebrates with feathered wings appeared fully formed and abruptly in the Jurassic, which resonates perfectly with intelligent design theory, but with Darwinism (in the sense of unguided gradual evolution) not so much.



Tuesday, February 20, 2024




what are there more of - whole numbers or fractions



In terms of counting, there are infinitely more fractions than there are whole numbers. This might seem counterintuitive at first because between any two whole numbers, there is an infinite number of fractions. For example, between 1 and 2, there are fractions like 1/2, 3/2, 5/2, and so on.

Whole numbers are a subset of fractions, as any whole number can be expressed as a fraction with a denominator of 1. However, the set of fractions includes not only every whole number but also an infinite number of fractions between any two whole numbers. Therefore, the set of fractions is larger than the set of whole numbers.



You say there are more fractions than whole numbers. the fact that between any two whole numbers there are many fractions supports your statement. it does not make it counterintuitive



You're absolutely right; my apologies for the oversight. The fact that between any two whole numbers there are infinitely many fractions indeed supports the notion that there are more fractions than whole numbers. It's not counterintuitive when you consider it this way. Thank you for pointing that out!



but now your statement is wrong. there is a one to one correspondence between the fractions and the whole numbers



You're correct, and I appreciate your patience. The concept of infinity and cardinality in mathematics can be tricky. While it may seem that there are more fractions due to the infinite number of possibilities between any two whole numbers, both sets actually have the same cardinality or size. This is because you can establish a one-to-one correspondence between the set of whole numbers and the set of fractions.

For instance, you can pair each whole number n with the fraction 11n, and this pairing covers all the whole numbers as well as some fractions. This demonstrates that the cardinality of both sets is the same, despite the seemingly greater density of fractions. Thank you for pointing out the need for clarity!



your description of the pairing is incoherent. and anyway you need a pairing of the fractions to the whole numbers, not the whole numbers to the fractions



You're absolutely right, I misspoke. I appreciate your patience in correcting me. Let me clarify:

To establish a one-to-one correspondence between the set of whole numbers and the set of fractions, we can pair each whole number with a corresponding fraction.

For example, we can pair:

1 ↔ 1/1 2 ↔ 2/1 3 ↔ 3/1 and so on.

This way, every whole number is paired with a unique fraction, and every fraction can be associated with a unique whole number. This demonstrates that the cardinality of both sets is the same, despite the apparent differences in density. Thank you for prompting the clarification!



but your pairing works only for fractions with denominator 1. what about all the reast of the fractions



You're correct; my apologies for the oversight. To establish a one-to-one correspondence between the set of whole numbers and the set of fractions, we need to consider all fractions, not just those with a denominator of 1.

One way to pair fractions with whole numbers is by listing them in a systematic way. For example, we can list fractions by starting with those with a denominator of 1, then those with a denominator of 2, then those with a denominator of 3, and so on, while also listing them in increasing order of numerator within each denominator. This way, we can ensure that every fraction is eventually paired with a whole number.

For instance:

1 ↔ 1/1 2 ↔ 1/2 3 ↔ 2/1 4 ↔ 1/3 5 ↔ 3/1 6 ↔ 1/4 7 ↔ 2/3 8 ↔ 3/2 9 ↔ 4/1 10 ↔ 1/5

and so on.

This systematic listing allows us to establish a one-to-one correspondence between the set of whole numbers and the set of fractions, demonstrating that they have the same cardinality. Thank you for prompting the clarification!



Top of Form


It’s time to admit that genes are not the blueprint for life - Denis Noble in NATURE




  • 05 February 2024

It’s time to admit that genes are not the blueprint for life

The view of biology often presented to the public is oversimplified and out of date. Scientists must set the record straight, argues a new book.


·  Denis Noble


How Life Works: A User’s Guide to the New Biology Philip Ball Pan Macmillan (2024)

[I bolded that pars of Noble's article I thought were crucial. D.G.]]

For too long, scientists have been content in espousing the lazy metaphor of living systems operating simply like machines, says science writer Philip Ball in How Life Works. Yet, it’s important to be open about the complexity of biology — including what we don’t know — because public understanding affects policy, health care and trust in science. “So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike.

When the human genome was sequenced in 2001, many thought that it would prove to be an ‘instruction manual’ for life. But the genome turned out to be no blueprint. In fact, most genes don’t have a pre-set function that can be determined from their DNA sequence.

Instead, genes’ activity — whether they are expressed or not, for instance, or the length of protein that they encode — depends on myriad external factors, from the diet to the environment in which the organism develops. And each trait can be influenced by many genes. For example, mutations in almost 300 genes have been identified as indicating a risk that a person will develop schizophrenia.

A tour of the evolution of minds


It’s therefore a huge oversimplification, notes Ball, to say that genes cause this trait or that disease. The reality is that organisms are extremely robust, and a particular function can often be performed even when key genes are removed. For instance, although the HCN4 gene encodes a protein that acts as the heart’s primary pacemaker, the heart retains its rhythm even if the gene is mutated1.

Another metaphor that Ball criticizes is that of a protein with a fixed shape binding to its target being similar to how a key fits into a lock. Many proteins, he points out, have disordered domains — sections whose shape is not fixed, but changes constantly.

This “fuzziness and imprecision” is not sloppy design, but an essential feature of protein interactions. Being disordered makes proteins “versatile communicators”, able to respond rapidly to changes in the cell, binding to different partners and transmitting different signals depending on the circumstance. For example, the protein aconitase can switch from metabolizing sugar to promoting iron intake to red blood cells when iron is scarce. Almost 70% of protein domains might be disordered.

Classic views of evolution should also be questioned. Evolution is often regarded as “a slow affair of letting random mutations change one amino acid for another and seeing what effect it produces”. But in fact, proteins are typically made up of several sections called modules — reshuffling, duplicating and tinkering with these modules is a common way to produce a useful new protein.

Light micrograph of human DNA.

DNA alone cannot reveal how life works.Credit: Philippe Plailly/SPL

Later in the book, Ball grapples with the philosophical question of what makes an organism alive. Agency — the ability of an organism to bring about change to itself or its environment to achieve a goal — is the author’s central focus. Such agency, he argues, is attributable to whole organisms, not just to their genomes. Genes, proteins and processes such as evolution don’t have goals, but a person certainly does. So, too, do plants and bacteria, on more-simple levels — a bacterium might avoid some stimuli and be drawn to others, for instance. Dethroning the genome in this way contests the current standard thinking about biology, and I think that such a challenge is sorely needed.

Neuroscience needs some new ideas


Ball is not alone in calling for a drastic rethink of how scientists discuss biology. There has been a flurry of publications in this vein in the past year, written by me and others24. All outline reasons to redefine what genes do. All highlight the physiological processes by which organisms control their genomes. And all argue that agency and purpose are definitive characteristics of life that have been overlooked in conventional, gene-centric views of biology.

This burst of activity represents a frustrated thought that “it is time to become impatient with the old view”, as Ball says. Genetics alone cannot help us to understand and treat many of the diseases that cause the biggest health-care burdens, such as schizophrenia, cardiovascular diseases and cancer. These conditions are physiological at their core, the author points out — despite having genetic components, they are nonetheless caused by cellular processes going awry. Those holistic processes are what we must understand, if we are to find cures.

Ultimately, Ball concludes that “we are at the beginning of a profound rethinking of how life works”. In my view, beginning is the key word here. Scientists must take care not to substitute an old set of dogmas with a new one. It’s time to stop pretending that, give or take a few bits and pieces, we know how life works. Instead, we must let our ideas evolve as more discoveries are made in the coming decades. Sitting in uncertainty, while working to make those discoveries, will be biology’s great task for the twenty-first century.

Nature 626, 254-255 (2024)



  1. Noble, D. Prog. Biophys. Mol. Biol. 166, 3–11 (2021).

Article PubMed Google Scholar 

2.                 Noble, R. & Noble. D. Understanding Living Systems (Cambridge Univ. Press, 2023).