The use of random procedures in describing non-random aspects of the world

 It has often been argued that quantum mechanics is no help to support free will because, although it does deny absolute determinism, it only puts random occurrence of events as an alternative, and randomness cannot support the idea of free will. This thought is usually based on an assumption that randomness is somehow without meaning, without significance, without reference to anything substantially real. The two articles below I think make that assumption untenable.

The Counterintuitive Power of Randomness By JORDANA CEPELEWICZ

 

Sometimes an idea’s time arrives. In the late 1940s, the idea that randomness can be a powerful tool arrived in New Jersey. Claude Shannon, an electrical engineer at the Bell Telephone Laboratories in Murray Hill, used random codes to show that it is possible to transmit information over arbitrarily noisy channels. Independently, Paul Erdős, a Hungarian mathematician working at the Institute for Advanced Study, some 30 miles to the southwest, used arguments depending on randomness to prove a seminal result in graph theory. Mathematical graphs are collections of points with lines connecting some of them. Erdős showed that in small enough graphs, it’s possible to avoid creating groups of points, called cliques, that are all connected or all disconnected.  In physics, the role of randomness had undergone a profound change during the previous generation, as the discovery of quantum mechanics indicated that the universe is inherently random. But while physicists saw randomness as a challenge to be overcome, mathematicians and engineers figured out how to put it to use. As Rahul Santhanam of the University of Oxford explained, there’s something paradoxical about the way randomness helps mathematicians solve problems. They often use it to prove that a given mathematical structure exists without specifying how to build it. For example, Erdős’ proof of the existence of clique-less graphs didn’t specify how to make them. Instead, he showed that if you consider the set of all possible graphs of a given size, and choose one at random, the chance that you’ll find a graph without a “forbidden” clique is greater than zero. Which means that such a graph must exist. Shannon’s result was the beginning of a discipline called information theory, which explores how much information can theoretically be transmitted in particular circumstances — though it does not necessarily spell out the best way to do so. Like Erdős, Shannon didn’t specify how to create a scheme for reliable transmission over a noisy channel. But, using randomness, he proved that such a way must exist. Since then, mathematicians have used randomness as a tool not just in graph theory and information theory, but also in geometry, analysis (an advanced form of calculus), combinatorics (the study of counting methods) and computer science. Earlier this year, Avi Wigderson of the Institute for Advanced Study won a Turing award, one of the top honors in computer science, in part for his work studying connections between randomness and computation. In recent years, mathematicians have been probing the limits of probabilistic methods and gaining intuition for where they might fail. “It’s very, very natural to try to use randomness to try to push things through,” one mathematician told me. However, “randomness only gets you so far.”    What’s New and Noteworthy Still, it gets you very, very far. Researchers have continued to follow in Erdős’ footsteps, using randomness to prove many results in an area called Ramsey theory, which studies the unavoidable formation of cliques in graphs. In 2020, for instance, two mathematicians improved the lower bound on numbers that quantify how big a graph must get before certain patterns become inevitable. The following year, Quanta reported on a proof that marked major progress toward resolving one of the oldest problems in Ramsey theory, a question about how long disordered strings can be. And last year, I wrote about yet another Ramsey result where randomness was crucial. Probabilistic methods have also made it possible to prove the existence of other kinds of structures. In 2017, mathematicians heaped one random process on top of another, only to find that consistent geometric patterns arise amid all that disorder. “The disorder converges to a universal form,” wrote Kevin Hartnett. “At the precise moment when a random system seems most chaotic, exquisite geometric order peers through.” Last year, I wrote about how mathematicians used a probabilistic method to prove that there are infinitely many configurations known as subspace designs — objects related to error-correcting codes — “whose existence is not at all obvious,” as one mathematician told me. In all this work, mathematicians have to be clever about how they employ randomness. In 2022, for instance, I covered a groundbreaking proof of the Kahn-Kalai conjecture, a major problem that asked when phase transitions occur in graphs and other systems. Two mathematicians gave the answer by randomly selecting pieces of graphs and sets until they gradually built up the structures they needed, rather than applying randomness in one fell swoop. Randomness seems like the very antithesis of everything math purports to be — the steadfast pursuit of logic, the search for patterns and structure, the crafting of neat and airtight arguments. And yet it’s become one of the subject’s most useful instruments.

 

 

 

 

Why the immune system takes its chances with randomness

https://www.nature.com/articles/nri3734-c1

• Philip D. Hodgkin, 
• Mark R. Dowling & 
• Ken R. Duffy 

Nature Reviews Immunology volume 14, page711 (2014)Cite this article

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In their recent Opinion article (Lymphocyte fate specification as a deterministic but highly plastic process. NatureRev.Immunol.http://dx.doi.org/10.1038/nri3734(2014))¹, Reiner and Adams presented a fascinating deterministic interpretation of how lymphocytes acquire different fates. They propose that the generation of multiple lymphocyte subsets from each precursor occurs via an inevitable developmental pathway. This deduction is based on the premise that the system is too important to be left to stochastic processes. To account for recent evidence to the contrary, stochastic processes are suggested to only appear under conditions in which artificially large numbers of responding precursors might relax the deterministic programme (as used in Refs 2,3) or under in vitro conditions in which the usual three-dimensional (3D) arrangement of externally delivered signals that channel fates is removed (as used in Ref. 4). In other words, stochastic mechanisms only occur when experimental conditions happen to support the role of randomness.

There are, however, several reasons — as outlined below — to challenge the premise that stochastic processes are not equally up to the task of generating a reliable immune response.

Precedent

The authors themselves point out that evolution exploits randomness for the most important task of all — creating lymphocyte receptor diversity. Other immune examples of stochastic processes include the probabilistic expression of cytokines^5,6 and the combinatorial expression of natural killer cell receptors in a population⁷.

Efficiency

In the imagined B cell and T cell odysseys¹, at least six intricate moves must take place to generate the different cell fates. A distinct deterministic pathway is needed for each, and the correct set of signals must be received in the correct order by each of potentially thousands of progeny; lymphocytes and numerous other cells must encode complex instructions for orchestrating the right set of signals to generate every cell type at the right time. By contrast, by using stochastic processes multiple cell types can be generated with much simpler instructions^4,8,9,10,11, even in the absence of environmental direction.

Reductionism

It is tempting to observe the complex structures and cell interactions of primary lymphoid tissue and deduce that they are crucial for the formation of heterogeneous outcomes. This hypothesis has been tested by asking what remains when such structures are removed. We and others find a great deal of cell fate heterogeneity under simple in vitro culture conditions^4,5,6,12,13. Conversely, crucial molecular contributors to early developmental programmes, including asymmetric cell division, do not alter B cell or T cell responses in vivo¹⁴. Thus, although the 3D environment and asymmetric programming might have some role in modifying cell fate allocation, they are not the only sources of variation.

Extrapolation

In the stochastic interpretation, variation is inherent and consistent immune outcomes only arise when considering the population as a whole. As Reiner and Adams point out, the number of antigen-specific precursors recruited into the immune response is a crucial variable, and may be as low as 20. However, mathematical models in which randomness drives cell fate selection suggest that a reasonably robust immune response can be achieved even with starting cell numbers of this order^4,9,10,15. Thus, a role for randomness should not be rejected on this basis alone.

Summary

As a research community, we have not yet acquired all of the data required to answer how both deterministic and stochastic processes interleave to build the complete immune response. However, along with Reiner and Adams, we look forward to the resolution of this conundrum. Perhaps unlike them, however, we are gamblers, suspecting that the immune system does play a game of chance, albeit with the rules having evolved so that the odds are stacked in our favour.

References

1. Reiner, S. L. & Adams, W. C. Lymphocyte fate specification as a deterministic but highly plastic process. Nature Rev. Immunol. http://dx.doi.org/10.1038/nri3734 (2014).
2. Buchholz, V. R. et al. Disparate individual fates compose robust CD8⁺ T cell immunity. Science 340, 630–635 (2013).

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3. Gerlach, C. et al. Heterogeneous differentiation patterns of individual CD8⁺ T cells. Science 340, 635–639 (2013).

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4. Duffy, K. R. et al. Activation-induced B cell fates are selected by intracellular stochastic competition. Science 335, 338–341 (2012).

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5. Guo, L., Hu-Li, J. & Paul, W. E. Probabilistic regulation in TH2 cells accounts for monoallelic expression of IL-4 and IL-13. Immunity 23, 89–99 (2005).

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7. Raulet, D. H. et al. Specificity, tolerance and developmental regulation of natural killer cells defined by expression of class I-specific Ly49 receptors. Immunol. Rev. 155, 41–52 (1997).

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8. Rohr, J. C., Gerlach, C., Kok, L. & Schumacher, T. N. Single cell behavior in T cell differentiation. Trends Immunol. 35, 170–177 (2014).

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9. Duffy, K. R. & Hodgkin, P. D. Intracellular competition for fates in the immune system. Trends Cell Biol. 22, 457–464 (2012).

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10. Subramanian, V. G., Duffy, K. R., Turner, M. L. & Hodgkin, P. D. Determining the expected variability of immune responses using the cyton model. J. Math. Biol. 56, 861–892 (2008).

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11. Hodgkin, P. D. A probabilistic view of immunology: drawing parallels with physics. Immunol. Cell Biol. 85, 295–299 (2007).

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12. Hasbold, J., Corcoran, L. M., Tarlinton, D. M., Tangye, S. G. & Hodgkin, P. D. Evidence from the generation of immunoglobulin G-secreting cells that stochastic mechanisms regulate lymphocyte differentiation. Nature Immunol. 5, 55–63 (2004).

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13. Bird, J. J. et al. Helper T cell differentiation is controlled by the cell cycle. Immunity 9, 229–237 (1998).

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14. Hawkins, E. D. et al. Regulation of asymmetric cell division and polarity by Scribble is not required for humoral immunity. Nature Commun. 4, 1801 (2013).

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Acknowledgements

P.D.H. and M.R.D. are supported by National Health and Medical Research Council (NHMRC) Fellowships and NHMRC grants 1057831 and 1054925, and Independent Research Institutes Infrastructure Support Scheme Grant 361646. K.R.D. is supported by Science Foundation Ireland grant 12 IP 1263. P.D.H. and K.R.D. are also supported by the Human Frontier Science Program, grant RGP0060/2012.

Author information

Authors and Affiliations

1. and the Department of Medical Biology, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, 3052 Victoria, Australia, University of Melbourne, Melbourne, 3010 Victoria, Australia.,

Philip D. Hodgkin & Mark R. Dowling

2. Hamilton Institute, National University of Ireland, Maynooth, County Kildare, Ireland

Ken R. Duffy

Corresponding author

Correspondence to Philip D. Hodgkin.

 

How science is - and should not be - done

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

Günter Bechly

April 5a Commons.

https://evolutionnews.org/2024/04/fossil-friday-new-study-confirms-feathered-dinosaurs-were-secondarily-flightless-birds/

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.

References

• Feduccia A 1980. The Age of Birds. Harvard University Press, Cambridge (MA), ix+196 pp.
• Feduccia A 1996. The Origin and Evolution of Birds. Yale University Press, New Haven (CT), 420 pp. 
• Feduccia A 2012. Riddle of the Feathered Dragons: Hidden Birds of China. Yale University Press, New Haven (CT), x+358 pp.
• Feduccia A 2020. Romancing the Birds and Dinosaurs: Forays in Postmodern Paleontology. Brown Walker Press, Irvine (CA), 336 pp.
• Field Museum 2024. The hidden rule for flight feathers and how it could reveal which dinosaurs could fly. Phys.org February 12, 2024. https://phys.org/news/2024-02-hidden-flight-feathers-reveal-dinosaurs.html
• Geist N 2022. Romancing the Birds and Dinosaurs: Forays in Postmodern Paleontology. Ornithology 139(3), 1–2. DOI: https://doi.org/10.1093/ornithology/ukac013
• James FC 2021. How Many Dinosaurs Are Birds? Bioscience 71(9), 991–994. DOI: https://doi.org/10.1093/biosci/biab060
• Kiat Y & O’Connor JK 2024. Functional constraints on the number and shape of flight feathers. PNAS 121(8): e2306639121. DOI: https://doi.org/10.1073/pnas.2306639121
• Koumoundouros T 2024. Scientists Discover an Ancient Pattern Hidden in The Feathers of Birds. ScienceAlert February 25, 2024. https://www.sciencealert.com/scientists-discover-an-ancient-pattern-hidden-in-the-feathers-of-birds
• Leigh EG 2014. Alan Feduccia’s Riddle of the Feathered Dragons: what reptiles gave rise to birds? Evolution: Education and Outreach 7: 9, 1–3. DOI: https://doi.org/10.1186/s12052-014-0009-0
• Ostrom JH 1994. On the origin of birds and of avian flight. pp. 160–177 in: Prothero DP & Schoch RS (eds). Major Features of Vertebrate Evolution. University of Tennessee Press, Knoxville (TN), 270 pp.
• Ruben J 1997. The fuss over feathers. BioScience 47(6), 392–395. DOI: https://doi.org/10.2307/1313154
• University of Tokyo 2023. How birds got their wings. Phys.org February 24, 2023. https://phys.org/news/2023-02-birds-wings.html
• Uno Y & Hirasawa T 2023. Origin of the propatagium in non-avian dinosaurs. Zoological Letters 9: 4, 1–8. DOI: https://doi.org/10.1186/s40851-023-00204-x