Theism:the mother of modern science?

 

Genesis II: The sequel?

 

On Darwinian mythmaking and mythbusting.

 A New Scholarly Book Trying to Debunk Myths about Charles Darwin and His Theory

Richard Weikart

In a new book published by Cambridge University Press, Darwin Mythology: Debunking Myths, Correcting Falsehoods, an array of prominent Darwin scholars attempt to dismantle 24 myths about Darwin and his theory. Many of these essays are excellent examples of historians setting the record straight. However, while myth-busting is a venerable pursuit for historians, caution must be exercised, especially when dealing with ideologically loaded subjects. Indeed, ironically, in a few cases in this volume, which I will discuss in subsequent posts, the debunkers need to be debunked themselves, because instead of correcting falsehoods, they end up creating or perpetuating falsehoods.

Problems with “Mythology”

Indeed, the whole notion of mythology can at times be problematic, because some scholars brand as “myth” interpretations of other scholars with whom they disagree. For example, James G. Lennox, in his chapter on Darwin and teleology (which I will discuss in a subsequent post), informs us that the Darwinian biologist Michael Ghiselin has dubbed as myth the view that Darwin’s theory included teleology. Lennox states, “In this chapter, then, my aim is to show that what Michael Ghiselin claims to be a myth is in fact reality, and that his assertion that Darwin rid biology of teleology is itself a myth.” (p. 183) So here we have two scholars insisting that the other one is embracing a myth.

A related problem is that in some cases, the scholars in this volume disagree among themselves on what is mythical. For example, David Depew in his essay claims that in addition to natural selection, Darwin also believed in group selection. (p. 177) In his essay on Darwin and race, Erik L. Peterson seems to agree, strongly implying that Darwin believed in group selection. (p. 255) The late Michael Ruse, however, in trying to distance Darwin from Alfred Russel Wallace, claims rather emphatically that Darwin rejected group selection. (pp. 133-34)

So, Which Is the Myth?

On this particular issue of group selection, it seems to me that Ruse is the one perpetuating a misconception about Darwin. Ruse uses rather twisted logic to maintain his position. After quoting a passage in Descent of Man where Darwin discusses tribes competing with other tribes (which is group selection), Ruse makes the bizarre claim that this is not really group selection. Why not? Well, Ruse informs us that right after this discussion of tribes competing, Darwin promoted what we call today “reciprocal altruism.” Therefore, Ruse oddly asserts, Darwin could not be promoting the idea of group selection. (I should note that Ruse is wrong about the placement of this passage, as it actually comes three pages earlier than the one about the tribes, but this is a minor point). Ruse’s logic is fallacious, because group selection and reciprocal altruism are not contradictory. Darwin believed them both. No wonder Depew and Peterson disagree with Ruse, as do a host of other Darwin scholars.

Before I critique the other essays that are problematic, let me draw attention to some of the myths about Darwin that this volume properly addresses. John Hedley Brooke refutes the myth that the biologist Thomas Henry Huxley demolished Anglican Bishop Samuel Wilberforce at their famous 1860 debate before the British Association for the Advancement of Science. It seems that the debate (or discussion) was more of a toss-up. I was surprised to learn from Brooke’s essay that one scientist who had embraced Darwinism before this event actually abandoned Darwinism as a result of the discussion that day. (p. 151)

White Supremacy and Genocide

An interesting essay by Erik L. Peterson refutes the myth that Darwin believed in racial equality. Peterson acknowledges that Darwin hated slavery, but shows that it was not because he believed in racial equality. Both in Descent of Man and in his correspondence Darwin not only clearly expressed belief in the racial superiority of Europeans, but he insisted that the Europeans’ triumph in the racial struggle for existence — which would result in the racial extermination of allegedly inferior races — would bring evolutionary advance to the human species. In an 1860 letter to Lyell, Darwin stated, “White man is ‘improving off the face of the earth’ even races nearly his equal.” Right after quoting this, Peterson comments, “Here again, we might find jarring Darwin’s cavalier references to white supremacy and genocide as supportive of his overall theory.” (p. 254)

In another essay Richard W. Burkhardt Jr. counters the widespread idea that Darwin rejected Lamarck’s ideas about use and disuse and the inheritance of acquired characteristics. To be sure, Burkhardt explains that Darwin stressed the primacy of natural selection and considered Lamarckian mechanisms secondary. However, Darwin did not dismiss them outright, as some later Darwinians, such as the German biologist August Weismann, did.

John Van Whye makes a strong case against the claim that Darwin delayed publication of The Origin of Species for twenty years, allegedly because he was afraid to make his views public. Van Whye shows that Darwin divulged his theory to many of his contemporaries in his correspondence. None of Darwin’s family or contemporaries ever claimed that Darwin delayed publishing his theory. Indeed, the idea that he delayed only arose in the mid 20th century. During those twenty years between discovering his theory and publishing it, Darwin was studying and doing research to buttress and refine his theory.

Just a Sampling

This is just a sampling of the many interesting and useful essays in this work. However, as I indicated, some of the essays are problematic, and I will address a few of these in the coming days.

The throne of JEHOVAH'S Son demystified.(yet again)

 RS reads: “Of the Son he says, ‘Thy throne, O God, is for ever and ever.’” (KJ, NE, TEV, Dy, JB, NAB have similar renderings.) However, NW reads: “But with reference to the Son: ‘God is your throne forever and ever.’” (AT, Mo, TC, By convey the same idea.)

Which rendering is harmonious with the context? The preceding verses say that God is speaking, not that he is being addressed; and the following verse uses the expression “God, thy God,” showing that the one addressed is not the Most High God but is a worshiper of that God. Hebrews 1:8 quotes from Psalm 45:6, which originally was addressed to a human king of Israel. Obviously, the Bible writer of this psalm did not think that this human king was Almighty God. Rather, Psalm 45:6, in RS, reads “Your divine throne.” (NE says, “Your throne is like God’s throne.” JP [verse 7]: “Thy throne given of God.”) Solomon, who was possibly the king originally addressed in Psalm 45, was said to sit “upon Jehovah’s throne.” (1 Chron. 29:23, NW) In harmony with the fact that God is the “throne,” or Source and Upholder of Christ’s kingship, Daniel 7:13, 14 and Luke 1:32 show that God confers such authority on him.

Hebrews 1:8, 9 quotes from Psalm 45:6, 7, concerning which the Bible scholar B. F. Westcott states: “The LXX. admits of two renderings: [ho the·osʹ] can be taken as a vocative in both cases (Thy throne, O God, . . . therefore, O God, Thy God . . . ) or it can be taken as the subject (or the predicate) in the first case (God is Thy throne, or Thy throne is God . . . ), and in apposition to [ho the·osʹ sou] in the second case (Therefore God, even Thy God . . . ). . . . It is scarcely possible that [’Elo·himʹ] in the original can be addressed to the king. The presumption therefore is against the belief that [ho the·osʹ] is a vocative in the LXX. Thus on the whole it seems best to adopt in the first clause the rendering: God is Thy throne (or, Thy throne is God), that is ‘Thy kingdom is founded upon God, the immovable Rock.’”—The Epistle to the Hebrews (London, 1889), pp. 25, 26

The inference to the best explanation.

 

The ongoing search for the fountain of youth.

 

In search of a new physics?

 

Why asymetric warfare is not favoring palestinian nationalists.

 

The future of war.

 

Neanderthals: disinherited no more?

 

The beginning?

 

Toward a scientifically rigorous design inference

 

The conserved optimality of vertebrate limbs vs. Darwin.

 

Primordial WiFi?

 Biological Information in Static Electricity

David Coppedge

Insects and spiders know how to read the air when static electricity is present. Electrical charge, to them, is a source of biological information, says Daniel Robert in Current Biology in his Primer on “Aerial Electroreception.”

This newfound sensory modality reveals a previously unrecognised source of information, a new informational ecological niche integral to diverse life histories and navigational abilities, which remarkably involves animals, plants and atmospheric electricity

Arthropods live in an “electric ecology” where “electrostatics is everywhere, always, and all at once.” They come equipped with antennae and tiny hairs that are sensitive to the electrical environment. Sensing a charge, however, is only a part of the story. How do these organisms utilize the information? What does it tell them? How does it trigger a response?

Coulomb’s Law

In a brief review of electrostatics (as opposed to electrodynamics, which involves charges moving near the speed of light), Dr. Robert discusses electric fields and Coulomb’s Law — the principle that like charges repel and opposite charges attract. He notes that “electric fields are ubiquitous in the presence of matter.” He then links electrosensitive abiotic materials with electrosensitive biological materials.

In essence, electrostatics provides a framework for understanding how a static imbalance in charge distribution can ensue between materials, and how forces arise from it. Biological materials are evidently not exempt from such processes, and it is proposed here that electrostatics plays a discrete yet pervasive and significant role in the informational ecology of terrestrial organisms.

Those terrestrial organisms include plants. Flowering plants can fashion the electric ecology for pollinators, as I discussed in an article about floral electric fields that attract bumblebees. See also my article, “Bioelectricity Gives Biologists a Jolt.” Professor Robert’s article extends the concept of the electric ecology to wider dimensions.

While humans are only weakly sensitive to electrostatic charges in air, those charges are large for small organisms like arthropods. “It has become increasingly clear that many organisms tend to be electrically charged,” he says. In fact, “it is actually very difficult to find objects, biological or else, that are not charged.” A flying insect, therefore, can “feel” the electrical field in its environment with its sensory equipment and react if it has the mechanical equipment and brain software to know how to use the information.

Crucially, these ubiquitous electrical fields generate the Coulomb forces between charged objects that are measurable and putatively useful to organisms. Thus, do electric fields have the potential to be a source of information for animals and plants to organise their lives in space and time?

The Answer Is Yes

The influence of static charge in pollination is one demonstrable case — not only for bees, but for moths and hummingbirds as well. A flower, “grounded” to ground (a net source of electrons), attracts a bee that accumulates a positive charge flying through air. The apex of the plant will be the most negatively charged due to the atmospheric potential gradient (APG) that increases the electric potential 100V for every meter above ground. While the Coulomb attraction would be too weak to move the entire insect, its sensory hairs and antennae feel a tractor beam drawing them to the flower. 

Charges without sensors cannot use information in the electric ecology. But with its tiny hairs, antennae, and wings which “can act as charged dielectric surfaces,” the insect might be able to carry and store electrical information for communicating with other bees in the hive. This fascinating and only recently investigated phenomenon is probably true of most arthropods since all are equipped with similar sensors.

In effect, these structures are present in nearly all species of terrestrial arthropods. The notion thus arises that such processes of aerial electroreception may be widespread, though other mechanisms of detection cannot be excluded. It can be highlighted that these sensory hairs can be sensitive to air currents and sounds, in addition to electric fields. Here, it is expected that hairs, as long, thin, sharp and protruding structures, will tend to accumulate charge and engage in electrostatic interactions. Hair canopies constitute a distributed array of sensors, sometimes covering the entire arthropod body. Theoretical work shows that dual acoustic and electric detection of hair arrays can extract rich information, sensing the position and distance of external charges.

Other Examples of Electroreception 

Professor Robert gives other examples of electroreception. A caterpillar might sense the approach of a wasp. “Reciprocally, the capacity of wasps to detect caterpillars electrostatically should be considered,” he writes, “which also raises the enticing possibilities of electric crypsis, masquerade, and/or aposematism.” Spiders that use ballooning with silk threads to travel long distances might be utilizing Coulomb forces to lift themselves up through the APG. And unfortunately for large mammals, their fur can accumulate thousands of volts, potentially helping parasites like ticks ride the electrostatic tractor beam to their skin.

These are just a few of the research possibilities in the new field of aerial electroreception. Professor Robert’s article is intriguing, but sadly, he attributes causal powers to evolution, committing the fallacy that evolution searches for phenomena to exploit. The maxim “opportunity knocks” works for humans with foresight, but mutations and natural selection couldn’t care less if static electricity is in the air or not. Without operational sensors and instincts built into an organism from the start, nothing would happen.

A braver newer world than ever?

 

Moore's Law redux?

 

The OoL just got less simple?

 

Einstein's feet of clay?

 

EVs :the fine print.

 

His Name will be published in all the earth.

 

The "equilbrium" in "punctuated equilibrium" ?

Fossil Friday: Evolutionary Stasis in Beetles

Gunter Bechly 

This Fossil Friday features the living ground beetle genus Loricera, which has recently been recovered as fossil adults and larvae from mid-Cretaceous Burmese amber. The genus belongs to the ground beetle family Carabidae and features in adults as well as the larval stage specially modified antennae and mouth parts for predation on springtails (Collembola) in leaf litter. Spiny hairs at the base of the antennae and the maxillae serve as a kind of catching cage for their springtail prey. This complex adaptation has now turned out to be much more ancient than expected.

In two recent papers Li et al. (2024a, 2024b) described adult and larval Loricera beetles from the mid-Cretaceous Kachin amber (Burmite) of Myanmar, which has been radiometrically dated to an age of 99 million years. These fossil beetles are basically indistinguishable from the various living species of the genus Loricera and have identical anatomical features of adults and larvae. This means that this beetle with its unique adaptations existed in unchanged form since at least about 100 million years and survived the mass extinction at the end of the Cretaceous period.

The Crucial Point

A popular science article in Wired (Kahil 2024) freely admits that “the Loricera beetle’s survival story challenges conventional notions of evolution” and exhibits “a remarkable consistency in an ever-changing world.” This is indeed the crucial point, because such striking cases of stasis are commonly explained away by evolutionary biologists as due to stabilizing selection in a stable environment of their ecological niche. However, this explanation simply is not plausible over hundreds of millions of years with changing habitats, changing climate, changing biota, and even mass extinction events of apocalyptic dimensions. The press release (NIGPAS 2024) reporting the new discovery acknowledges that “the K/Pg mass extinction triggered one of the most profound biodiversity reorganizations in geological history,” but still “the study suggests that both springtails and their predators have exhibited significant evolutionary stasis, both in terms of individual species morphology and community structure.”

Compare this with the evolutionist’s claim that pig-like mammals similar to Indohyus and Pakicetus changed into fully marine dolphin-like whales such as Dorudon and Basilosaurus in just 4 to 8 million years. Natural selection is the great magician in evolutionary fantasy land, where it explains rapid change in explosive radiations as well as no change at all over eons in so-called “living fossils.” However, a theory that is always perfectly consistent with any possible outcome is not explaining anything, but rather is as dubious as Freudian psychoanalysis or astrology, with their vague predictions that always fit. And every fit is sold to the gullible public as a successful corroboration of the theory, which is why people still believe in astrology and — for what it’s worth — in unguided evolution through natural selection acting on random mutations. It is time to call neo-Darwinism out for what it indubitably is: a pseudoscience, which is nurtured, promoted, and fiercely defended by a gigantic industry in mainstream academia that depends on it!

References

Kahil N 2024. This black beetle is a survivor of the dinosaur extinction. Wired November 4, 2024. https://wired.me/science/this-black-beetle-is-a-survivor-of-the-dinosaur-extinction/

Li Y-D, Tihelka E, Engel MS, Huang & Cai C 2024a. Specialized springtail predation by Loricera beetles: An example of evolutionary stasis across the K-Pg extinction. The Innovation 5(3): 100601, 1–2. DOI: https://doi.org/10.1016/j.xinn.2024.100601

Li Y-D, Tihelka E, Engel MS, Xia F-Y, Huang D-Y, Zippel A, Tun KL, Haug GT, Müller P & Cai C-Y 2024b. Description of adult and larval Loricera from mid-Cretaceous Kachin amber (Coleoptera: Carabidae). Palaeoentomology 7(2), 265–276. DOI: https://doi.org/10.11646/palaeoentomology.7.2.10

NIGPAS 2024. Cretaceous Amber Reveals the Stability of Beetle-Specialized Predation. NIGPAS Newsroom September 25, http://english.nigpas.cas.cn/new/hs/rp/202409/t20240925_690552.html

ID :a fruitbearing tree.

Bad faith?

 

The human miracle vs. Darwin.

 

John ch.8:58 demystified (again)

 

It looks like technology because it is technology?

 The Eukaryotic Cell Cycle: An Irreducibly Complex System

Jonathan McLatchie

I have previously published several articles at Evolution News on the incredible design, and exquisite engineering, of the eukaryotic cell division cycle (see this recent article for links to previous essays on this subject). I also recently published a paper, in the journal BIO-Complexity, in which I documented significant obstacles to the origins of the eukaryotic cell cycle by evolutionary processes (available for free here).1 Here, I will describe several aspects of the cell cycle that render it irreducibly complex, which are also discussed in my paper.

Condensins

Condensins are protein complexes that play a crucial role in the organization and segregation of chromosomes during cell division. They are highly conserved across eukaryotes. Condensin I is active during late prophase and contributes to the structural integrity of chromosomes following the break-down of the nuclear envelope. Condensin II functions earlier in prophase and is involved in the initial stages of chromosome condensation in the nucleus.

Image source: Wikimedia Commons

Condensin molecules are composed of five subunits (as shown in the figure), including the SMC (Structural Maintenance of Chromosomes) proteins SMC2 and SMC4, which possess ATPase activity. SMC proteins possess coiled-coil domains (long, flexible arms that fold back on themselves, creating a V-shaped structure), a hinge domain that facilitates the dimerization of the two SMC proteins; and head domains containing ATP-binding and ATPase sites, energizing the activities of condensins. In addition to the SMC subunits, there are also three non-SMC subunits, which bind specific regions of DNA and assist in regulation of condensing activity.

Condensin complexes load onto chromatin in a stepwise manner, directed by non-SMC subunits. The SMC subunits create loops in DNA, utilizing their ATPase activity. These loops are stabilized and condensed into mitotic chromosomes.

The condensing proteins are crucial for the process of cell division. In their absence, the consequence would be chromosomal disorganization, as well as great difficulty in achieving proper segregation during mitosis.

Image credit: CNX OpenStax, CC BY 4.0 https://creativecommons.org/licenses/by/4.0, via Wikimedia Commons.

A complex of proteins, known as the kinetochore, assembles around the centromere of each chromosome (as shown in the figure), and is critical to the process of mitotic cell division. Each kinetochore serves as an attachment site for the spindle microtubules, which radiate from the centrosomes at the cell’s poles. Kinetochores assist with the alignment of chromosomes at the equatorial plane of the cell during metaphase, ensuring equal distribution of genetic material. Kinetochores also sense tension generated by microtubule pulling, thereby ensuring proper attachment. If improper attachments occur (e.g. if the kinetochores of both sister chromatids are attached to the same pole), these errors can be corrected by the kinetochore-associated machinery.

What would be the consequence if there were no kinetochores? This would result in the improper attachment of the chromosomes to the spindle apparatus, and the genetic material would be unequally distributed to the daughter cells. Indeed, so critical are the kinetochores to the process of cell division that they are found ubiquitously throughout all known eukaryotic organisms.

Separase and the Anaphase Promoting Complex

Image source: Wikimedia Commons.

Progression from metaphase to anaphase is mediated by the anaphase promoting complex or cyclosome (APC/C), an E3 ubiquitin ligase. When bound to its coactivator, Cdc20, the APC/C functions to ubiquitylate securin (a protein that prevents the cleavage of cohesin by the enzyme separase). Ubiquitylation of securin targets it for destruction by the cell’s molecular shredder, the proteasome. This liberates the enzyme separase to cleave the cohesin ring that tethers the sister chromatids together, thereby promoting sister chromatid separation.

In the absence of separase, the sister chromatids would fail to separate, and the cell would be rendered unable to segregate its chromosomes at anaphase. Indeed, experimental knockout studies have shown that deleting separase results in embryonic lethality.2,3 Cell cycle progression would also be halted in the absence of the APC/C, inhibiting the progression from metaphase to anaphase. Indeed, experimental studies knocking out APC2 (a core APC/C subunit) in mice, for example, resulted in lethal bone marrow failure within only seven days.4

Aurora Kinases

Aurora kinases are also crucial to proper spindle formation and chromosome segregation. Aurora kinase A phosphorylates proteins involved in microtubule organization and facilitates the accurate attachment of microtubules to kinetochores. Indeed, “Aurora A null nice die early during embryonic development during the 16-cell stage. These Aurora A null embryos have defects in mitosis, particularly in spindle assembly, supporting critical functions of Aurora A during mitotic transitions.”5 This indicates that Aurora kinase A is among the components that are essential for successful cell division.

Microtubules

I have previously described the critical role of microtubules in cell division. Microtubules radiate from centrosomes and anchor to the kinetochore complex, assembled around the centromere of each chromosome. During metaphase, the chromosomes are aligned along the equatorial plane of the cell, bound to microtubules at the kinetochore. In anaphase, the sister chromatids are pulled apart by the microtubules, driven by poleward spindle forces. The microtubules are, therefore, essential for segregating the sister chromatids into the two daughter cells.

In the absence of the microtubules, mitotic spindle assembly would thus be severely impaired, inhibiting chromosome alignment and segregation. Indeed, experimental studies with mouse embryos that are deficient in γ-tubulin exhibit a mitotic arrest that arrests development at the morula/blastocyst stages.6

The Contractile Ring

Image credit: David O Morgan, via Wikimedia Commons.

The contractile ring is also critical to the process of cytokinesis, the final stage of mitosis where the cell physically divides into two daughter cells. It is principally composed of actin filaments and myosin II motor proteins, together with other regulatory proteins such as formins, RhoA, and septins. These components form a dynamic, belt-like structure beneath the membrane at the equator of the dividing cell. The contractile ring produces the force that is needed for the ingression of the cleavage furrow. Myosin II proteins interact with actin filaments in the ring to generate this contractile force. This process is energized by hydrolysis of ATP. As the ring tightens, the plasma membrane is pinched inward, ultimately dividing the cytoplasm. The absence of the contractile ring would result in a failure of the cell to divide, leading to binucleated cells as well as other abnormalities.

Motor Proteins

In a previous article at Evolution News, I described the role of motor proteins (kinesin and dynein) in the assembly and function of the mitotic spindle during eukaryotic cell division. I’d refer interested readers to that essay for a discussion of this astounding process. The absence of these motor proteins would severely compromise the transport and positioning of chromosomes, resulting in chromosomal misalignment during metaphase and difficulty in establishing a proper mitotic spindle. The consequence would be errors in chromosome segregation during anaphase.

Cdk and Cyclin Molecules

I have written previously about the role of cyclin-dependent kinases and cyclin molecules in cell cycle progression. I refer readers there for a review. The Cdk and cyclin molecules exhibit redundancy, meaning that they are not all individually necessary. For example, mouse knockouts of Cdk2, 3, 4, or 6 still retain viability.7,8,9,10,11,12,13Furthermore, yeast cells possess only a single Cdk, specifically Cdk1.14 Interestingly, double knockouts involving combinations of Cdk2 and 4, or Cdk4 and 6, result in embryonic lethality, though a double knockout of Cdk2 and 6 does not.15,16 It appears, then, that the pair Cdk2 and 4 and the pair Cdk4 and 6 can substitute for one another.17 However, Cdk1 appears to be essential, and knocking it out arrests development at the blastocyst stage.18

Cdk molecules themselves are activated by the binding of cyclin molecules. Without those cyclins, the Cdks would be inactive, resulting in cell cycle arrest. Though there is redundancy here too (and thus not all cyclins are indispensable to successful division), the absence of cyclin B (which activates Cdk1 to drive progression into mitosis), would impair the transition from G2 to M phase. In other words, the cell could not enter mitosis. This is corroborated by experimental knockout studies of cyclin B in mouse embryos, leading to the arrest of the cell cycle in G2 after as little as two divisions.19,20

Checkpoints

I have written previously about the various cell cycle checkpoints — i.e., the G1 (restriction) checkpoint, G2 (DNA damage) checkpoint, and spindle assembly checkpoint (see my articles on these here, here and here). These are also essential for successful cell division. For instance, without the mitotic checkpoint complex, the cell’s ability to monitor spindle assembly would be abolished — drastically increasing the risk of cells proceeding through division with spindle defects, the result of which would be chromosome missegregation and aneuploidy. The absence of the G1 checkpoint would enable damaged DNA to enter S phase, which could lead to the propagation of mutations as well as genomic instability. The loss of the G2 checkpoint would allow cells with DNA damage to enter into mitosis, leading to the division of cells with unrepaired genetic material, as well as a greatly increased risk of chromosome aberrations. Without the DNA damage checkpoint in S phase, replication of damaged DNA would occur, resulting in the propagation of mutations and thus an elevated risk of genetic abnormalities in the daughter cells.

Irreducibly Complex

As seen from the cursory discussion above, various components of the mitotic cell division apparatus are indispensable for the system to work. This makes the eukaryotic cell division irreducibly complex, rendering it resistant to explanations in terms of blind, evolutionary processes. Any system that achieves a complex higher-level objective by means of various well-matched interacting components requires foresight to come about. In a subsequent article, I will discuss how the challenge to evolutionary accounts of the origins of eukaryotic cell division extends much deeper than this.

Notes

McLatchie J (2024) Phylogenetic Challenges to the Evolutionary Origin of the Eukaryotic Cell Cycle. BIO-Complexity 2024 (4):1–19 doi:10.5048/BIO-C.2024.4.

Kumada K, Yao R, Kawaguchi T, Karasawa M, Hoshikawa Y, et al (2006) The selective continued linkage of centromeres from mitosis to interphase in the absence of mammalian separase. J Cell Biol. 172(6): 835-46. doi:10.1083/jcb.200511126

Wirth KG, Wutz G, Kudo NR, Desdouets C, Zetterberg A, et al (2006) Separase: a universal trigger for sister chromatid disjunction but not chromosome cycle progression. J Cell Biol. 172(6): 847-60. doi:10.1083/jcb.200506119

Wang J, Yin MZ, Zhao KW, Ke F, Jin WJ, et al (2017) APC/C is essential for hematopoiesis and impaired in aplastic anemia. Oncotarget. 8(38): 63360-63369. doi:10.18632/oncotarget.18808

Lu LY, Wood JL, Ye L, Minter-Dykhouse K, Saunders TL, Yu X, Chen J (2008) Aurora A is essential for early embryonic development and tumor suppression. J Biol Chem. 283(46): 31785-90. doi:10.1074/jbc.M805880200

Yuba-Kubo A, Kubo A, Hata M, Tsukita S (2005) Gene knockout analysis of two gamma-tubulin isoforms in mice. Dev Biol.282(2): 361-73. doi:10.1016/j.ydbio.2005.03.031

Berthet C, Aleem E, Coppola V, Tessarollo L, Kaldis P (2003) Cdk2 knockout mice are viable. Curr Biol. 13: 1775–1785. doi:10.1016/j.cub.2003.09.024

Ortega S, et al. (2003) Cyclin-dependent kinase 2 is essential for meiosis but not for mitotic cell division in mice. Nat Genet.35: 25–31. doi:10.1038/ng1232

Ye X, Zhu C, Harper JW (2001) A premature-termination mutation in the Mus musculus cyclin-dependent kinase 3 gene. Proc Natl Acad Sci USA. 98: 1682–1686. doi:10.1073/pnas.98.4.1682Rane SG, et al. (1999) Loss of Cdk4 expression causes insulin-deficient diabetes and Cdk4 activation results in β-islet cell hyperplasia. Nat Genet. 22: 44–52. doi:10.1038/8751

Tsutsui T, et al. (1999) Targeted disruption of CDK4 delays cell cycle entry with enhanced p27Kip1 activity. Mol Cell Biol. 19: 7011–7019. doi:10.1128/MCB.19.10.7011

Hu MG, et al. (2009) A requirement for cyclin-dependent kinase 6 in thymocyte development and tumorigenesis. Cancer Res. 69: 810–818. doi:10.1158/0008-5472.CAN-08-2473

Malumbres M, et al. (2004) Mammalian cells cycle without the D-type cyclin-dependent kinases Cdk4 and Cdk6. Cell. 118: 493–504. doi:10.1016/j.cell.2004.08.002

Enserink JM, Kolodner RD (2010) An overview of Cdk1-controlled targets and processes. Cell Div. 5: 11. doi:10.1186/1747-1028-5-11

Malumbres M, et al. (2004) Mammalian cells cycle without the D-type cyclin-dependent kinases Cdk4 and Cdk6. Cell. 118: 493–504. doi:10.1016/j.cell.2004.08.002

Berthet C, Kaldis P (2007) Cell-specific responses to loss of cyclin-dependent kinases. Oncogene 26: 4469–4477. doi:10.1038/sj.onc.1210243

Satyanarayana A, Kaldis P (2009) Mammalian cell-cycle regulation: Several Cdks, numerous cyclins and diverse compensatory mechanisms. Oncogene. 28:2925–2939. doi:doi.org/10.1038/onc.2009.170

Diril MK, Ratnacaram CK, Padmakumar VC, Du T, Wasser M, Coppola V, Tessarollo L, Kaldis P (2012) Cyclin-dependent kinase 1 (Cdk1) is essential for cell division and suppression of DNA re-replication but not for liver regeneration. Proc Natl Acad Sci U S A. 109(10): 3826-31. doi:10.1073/pnas.1115201109

Berthet C, et al. (2006) Combined loss of Cdk2 and Cdk4 results in embryonic lethality and Rb hypophosphorylation. Dev Cell. 10: 563–573. doi:10.1016/j.devcel.2006.03.004

Strauss B, Harrison A, Coelho PA, Yata K, Zernicka-Goetz M, Pines J (2018) Cyclin B1 is essential for mitosis in mouse embryos, and its nuclear export sets the time for mitosis. J Cell Biol. 217(1): 179-193. doi:10.1083/jcb.201612147

On politics by other means.

 

Those time travelling birds again?

 Fossil Friday: New Fossil Stem Bird Is Surprisingly Modern

Gunter Bechly

This Fossil Friday features the bird Navaornis hestiae from the Late Cretaceous Adamantina Formation of southeastern Brazil, which is dated to an age of about 80 million years. This fossil was attributed to an extinct group called Enantiornithes, which thrived in many species around the globe in the Cretaceous period. The new taxon was just described this month by Chiappe et al. (2024) in the journal Nature. The discovery of this perfectly preserved fossil bird turned out be a kind of puzzle for evolutionary biologists, who study the history of bird origins.

The beautiful fossil even preserved detailed structures of the brain that could be studied with high-resolution CT scanning. A morphometrical analysis of the geometry of the brain placed Navaornis about midway between Archaeopteryx and modern birds. This is certainly interesting and arguably fits with the common evolutionary scenario. The authors of the new study say that “Navaornis exhibits a brain morphology intermediate between Archaeopteryx and crown birds along the main axis of endocranial shape variation” and thus “the morphology of the endocast of Navaornis shows an intermediate stage in the evolutionary history of the unique avian brain.” A news report in SciNews (News Staff 2024) quotes one of the authors with a comment that “the brain structure of Navaornis hestiae is almost exactly intermediate between Archaeopteryx and modern birds — it was one of these moments in which the missing piece fits absolutely perfectly.” Such a gem of course directly made it into the headline of the article that is titled ”80-Million-Year-Old Enantiornithine Fossil Fills Gap between Archaeopteryx and Modern Birds”.

So Far So Good

But there is a little complication. Even though entantiornithine birds are considered as stem birds because of several relatively “primitive” traits in their anatomy, the new species shows a remarkable similarity to modern birds that was quite unexpected for the scientists. The authors describe that the “cranial geometry of Navaornis shows an unprecedented degree of similarity between crown birds and enantiornithines” and note that “despite an overall geometry quantitatively indistinguishable from crown birds, the skull of Navaornis retains numerous plesiomorphies.” They admit this “implies that the origins of these ‘advanced’ traits often associated with crown birds either predated the origin of Ornithothoraces or evolved convergently among both Enantiornithes and crownward Euornithes.” They conclude as follows:

This degree of geometric convergence between Enantiornithes and crown birds suggests that developmental constraints responsible for canalizing the general shape of the bird skull may have been present throughout much of avian evolutionary history, predating both the phylogenetic divergence between Enantiornithes and Euornithes more than 130 million years ago as well as the evolutionary acquisition of several apomorphic characteristics of crown bird skull and brain morphology. The exceptionally well-preserved skull of Navaornis emphasizes the necessity of hitherto elusive undistorted Mesozoic bird skulls for illuminating the complex sequence by which the unique brains and skulls of modern birds arose.

Note the Crucial Word

Convergence means similarity not based on common descent, “may have been” means they have no clue, and “complex sequence” means that the data are not what they expected to find. Prior to this discovery none of the experts would have predicted such a modern skull in a “primitive” stem bird, but after the fact evolutionary biologists are always quick to offer a fancy just-so-story that reconciles the evidence with the theory.

It is quite remarkable that popular science reports such as an article in New Scientist (Woodford 2024) only emphasize that this “exquisite bird fossil provides clues to the evolution of avian brains”, and quotes one of the authors as saying that “Navaornis fills a roughly 70-million-year-long gap in our understanding of how the distinctive brains of modern birds evolved.” Reuters reports that this “’One-of-a-kind’ skull fossil from Brazil reveals bird brain evolution” (Dunham 2024). Is it really just a happy accident that there is no mention of the unexpected similarity of this alleged primitive bird to modern birds and the implied problems for bird evolution? Why do we mostly hear only one side of the story in the media? I suppose we must be protected from dangerous questions that could come up.

References

Chiappe LM, Navlón G, Martinelli AG, de Souza Carvalho I, Miloni Santucci R, Wu Y-H & Field DJ 2024. Cretaceous bird from Brazil informs the evolution of the avian skull and brain. Nature 635(8038), 376–381. DOI: https://doi.org/10.1038/s41586-024-08114-4

Dunham W 2024. ‘One-of-a-kind’ skull fossil from Brazil reveals bird brain evolution. Reuters November 13, 2024. https://www.reuters.com/science/one-of-a-kind-skull-fossil-brazil-reveals-bird-brain-evolution-2024-11-13/

News Staff 2024. 80-Million-Year-Old Enantiornithine Fossil Fills Gap between Archaeopteryx and Modern Birds. SciNews November 14, 2024. https://www.sci.news/paleontology/navaornis-hestiae-13425.html

Woodford J 2024. Exquisite bird fossil provides clues to the evolution of avian brains. New Scientist November 13, 2024. https://www.newscientist.com/article/2456043-exquisite-bird-fossil-provides-clues-to-the-evolution-of-avian-brains/

On mathematics antiDarwinian bias.

 Protein Designers Explore Sequence Space

David Coppedge

The twenty major amino acids used in life as we know it can be assembled in countless ways. What portion of that vast sequence space is functional? This question has had a long history among Darwin skeptics because the answer contributes to probability calculations for assessing the explanatory power of chance vs design for the origin of life.

Historical Background

The Wistar Institute symposium in 1966 has often been cited by ID advocates as a death knell for hopes that functional proteins would spontaneously arise by chance. Around this time in the late 1960s, about a decade after Francis Crick had proposed his famous “sequence hypothesis” for DNA and proteins, my father James F. Coppedge recognized the informational character of biomolecules. Working on a graduate degree in chemistry at UCLA, he attempted to estimate the “usable” portion of sequence space by analogy with useful combinations of letters in English words and sentences. He tested the analogy by searching through tens of thousands of random letters. In his 1973 book,1 he applied his rough estimate of useful text strings arising by random selections to argue for the extreme improbability of arriving at a single usable protein by chance, even granting a world-sized primordial soup of plentiful amino acids combining under ideal conditions at fantastically rapid rates. 

In 1984, Thaxton, Bradley and Olsen in their book The Mystery of Life’s Origin (updated in 2020), wrote about the formidable challenge of overcoming “configurational entropy” in sequence space. Douglas Axe, in his book Undeniable (2016), wrote about biochemistry experiments he performed to determine the limits of functionality by seeing how far a well-studied protein could be altered and still perform. His calculations, along with my father’s memorable “amoeba analogy” from his book (ch. 7) led to an episode in the Illustra Media film Origin (excerpted in their shorter video First Life).

William Dembski and Stephen Meyer have also discussed at length the informational nature of protein sequences and the probabilistic resources for accounting for them by chance in their books.2 Studies like these have all agreed that functional proteins occupy an infinitesimal fraction of sequence space, like a vanishingly small box in the corner of a sheet of graph paper.

The New Explorers

The arrival of AI tools such as AlphaFold that can predict protein folds for computer-generated polypeptides has opened up new ways to explore functional portions of sequence space outside of biology.3 In a fascinating News Feature in Nature on October 15, Ewen Callaway told about international contests to find new proteins. Promises of lucrative prizes are motivating explorers from around the world to join “protein-design competitions [that] aim to sift out the functional from the fantastical.” Notice the key word design:

Contests have driven key scientific advances in the past, particularly for the field of protein-structure prediction. This latest crop of competitions is drawing people from around the world into the related field of protein design by lowering the barrier to entry. It could also quicken the pace of validation and standards development and perhaps help to foster community. “It will push the field forward and test methods more quickly,” says Noelia Ferruz Capapey, a computational biologist at the Centre for Genomic Regulation in Barcelona, Spain.

The tournaments bypass the stodgy method of grant application, peer review and publication, speeding discovery and stimulating involvement. Callaway describes half a dozen competitions generating tens of thousands of candidate sequences, even from “people with no professional experience in biology” using their gaming computers at home.

Englert says that the high-quality entries from people who aren’t established researchers reminds him of the garage-tinkering origins of Apple, Microsoft and other tech giants. “It would have taken them two years of studying and joining a lab to get to the point where they can get started. Here they can do it over a weekend.” He imagines a future in which freelance protein designers vie for bounties set by companies, academic labs and others seeking a custom molecule.

Is This Evolution?

These contests are goal-directed with specific criteria, such as “looking for proteins capable of attaching to a growth hormone receptor called EGFR that is overactive in many cancers.” Another contest “tasked entrants with re-engineering an existing protein — a plant-virus enzyme used widely in protein purification — to make the molecule more efficient.”

Efforts at this kind of “directed evolution” have been around for a long time in labs. As Dembski explains in No Free Lunch and The Design Inference 2nd Ed, these “evolutionary algorithms” are not random searches comparable to natural selection, which must survive at each mutation, but intelligently guided, goal-directed projects. In the contests described by Callaway, success for the contestants is judged by a sequence’s match to a foreordained goal: it must fold, and it must bind to a specified molecule. A contestant may attempt random searches in sequence space but has the intelligence to determine whether a sequence meets the criteria.4 Even if the contestant does not know in advance what approach will be successful, he or she can perform an intelligently guided “search for a search” as if looking through a pile of treasure maps to identify which is best for locating a treasure.

It is misleading, therefore, to call a contest “Evolved 2024” or to name a new AI biology startup “EvolutionaryScale.” These have nothing to do with Darwinian evolution. This type of equivocation confuses the public. It resembles Darwin’s own blunder in comparing natural selection to artificial selection, a fallacy he continued all his life.5 

Intelligence Far Surpasses the Reach of Chance

The capabilities of intelligence over chance are profound. My father calculated that on average it would take chance 1,500 years (“If a person could draw and record one coin every five seconds day and night”) to arrange coins numbered one to ten in order—something an eight-year-old child could do in a few moments (p. 51). From there, he calculated how long it would take to expect success by chance at arranging the phrase “The Theory of Evolution” from a set containing lower- and uppercase letters and a space. The probability was 1 in 4.5 x 1039. Envisioning a machine attempting this project that could perform a billion draws per second at the speed of light, he concluded that the time required to expect one success would be 28 trillion times the assumed age of the earth. Then he compared it to the capabilities of a child:

So chance requires twenty-eight trillion times the age of the earth to write merely the phrase: “The Theory of Evolution,” drawing from a set of small letters and capitals as described, drawing at the speed of light, a billion draws per second! Only once in that time could the letters be expected in proper order.

Again, a child can do this, using sight and intelligence, in a few minutes at most. Mind makes the difference in the two methods. Chance really “doesn’t have a chance” when compared with the intelligent purpose of even a child. 

If chance had to rely on earthquakes and wind to do the job, it would never happen.6 

While we can hope for revolutionary insights from the contests to find new proteins, they will come about by intelligent design, not by evolution.

Notes

Coppedge, Dr James F, Evolution: Possible or Impossible? (Zondervan, 1973). This book was one of the few pre-ID Movement publications to use the phrase “intelligent design.” After eight printings, his popular and influential book went out of print but he self-published it through 2002. I have the remaining stock of copies for those interested. A digitized version is available at this link: http://crev.epoi 

Dembski, The Design Revolution (2004), ch 9-10; The Design Inference (2nd ed., 2023). Meyer, Signature in the Cell (2009), ch 8-10.

To make exploration of sequence space somewhat tractable, one must assume using only the canonical amino acids and assume they were already left-handed and join solely with peptide bonds at the proper linkages. Chance, of course, wouldn’t care about those details. 

Success depends on context. One of the longest meaningful alphabet sequences my father detected was “AGMCAP”—an imaginative stretch, but potentially useful in some contexts (p. 104). Protein sequences are even more demanding since they must fold and perform a useful function in three dimensions within a cell.

Robert Shedinger, Darwin’s Bluff (2024), p.71-78, 171-172, 199-200.

This is not an exaggerated claim. Dr. A. E. Wilder-Smith debunked the old Huxley analogy of a million monkeys typing Shakespeare given enough time with the observation that biochemical reactions are reversible. The monkey-typewriter analogy depends on assuming that the letters stay on the page. If they fall off soon after they are typed, a Shakespeare sonnet will never emerge. In biochemistry, peptide bonds fall apart in water. A growing random chain, therefore, would not survive for long in the best of real-world conditions, nor would any progress in the meaningful alphabet string survive the next quake or gust of wind.

Human kind Darwinism's most damaging explosion

 

Your tax dollars at work.

 

On the designed intelligence of the fruit fly.

 Design, Engineering, Specified Complexity: Appreciating the Fruit Fly Brain

Eric Cassell

Groundbreaking new research has documented the complexity and design of the brains of fruit flies (Drosphila melanogaster). Many of the results were published in a series of papers in the journal Nature. The basis for the research is the completion of the entire wiring diagram (called a connectome) of the fruit fly brain, which consists of 140,000 neurons.1 In addition, it includes more than 50 million connections (chemical synapses).2Keep in mind that, despite the number of neurons and connections, fruit fly brains are tiny, smaller than a poppy seed. Previously, researchers had mapped the brains of a few other organisms, including the roundworm C. elegans, however their brains consist of only 302 neurons. 

Most of the work was conducted by a group of researchers called the FlyWire consortium. The completion of the project and ongoing research is expected to result in a revolution in neuroscience. Previously it was believed that brains with hundreds of thousands of neurons were too large to map and assess function in much detail. But the results are a first step toward being able to do so, and potentially toward mapping at least segments of larger brains (including humans with more than 80 billion neurons and 100 trillion connections). The research has already revealed a number of important, and in some cases, surprising findings. 

Neuron Types

The research has identified at least 8,453 neuronal cell types.3 A neuron cell type is a group that has similar morphology and connectivity. This compares with the worm C. elegans which has 118 cell types.4 The research also identified different classes of neurons, depending upon their function. Examples include sensory neurons (labeled afferent) that send signals from sensory organs to the brain. Motor and endocrine neurons (labeled efferent) send signals from the brain to muscles and other organs.5

Previously, some theorized that brain neurons might be like “snowflakes,” that is, each one is unique. That would imply their development and connections are essentially a random process. However, the research confirms that is generally not the case. There is some evidence of randomness, as one analysis shows that, “Over 50% of the connectome graph is a snowflake. Of course, these non-reproducible edges [connections] are mostly weak.”6 The analysis does show that, “Neurons occasionally do something unexpected (take a different route or make an extra branch on one side of the brain). We hypothesize that such stochastic differences are unnoticed variability present in most brains…In conclusion, we have not collected a snowflake.”7 This means that the stronger connections are largely stereotyped and do not vary in a random manner significantly. Conversely, the findings show convincingly that neither is the brain structure a regular lattice type, as in crystals.

Complexity

Fruit flies exhibit a number of complex behaviors, including flight control (hovering, rapid changes in direction), navigation, mating courtship using pheromones, and swarming. Therefore, it isn’t that surprising that their brains show complexity. The average fruit fly neuron connection consists of 12.6 synapses.8 Individual neurons typically have less than 10 connections, but some have more than 100, and even a few have 1,000.9This means that there isn’t a uniform distribution of neurons or a uniform distribution of connections. The research has even been able to map the flow of information throughout the brain. The fruit fly brain consists of areas of specialized functions. These include visual processing, olfactory, auditory, mechanical sensors, and temperature sensors. A further indication of specialized functions is the report of one research project that analyzed 78 anatomically distinct “subnetworks” in the brain.10 This same analysis concluded, “The local structure of the brain displays a high degree of non-randomness, consistent with previous studies in C. elegans and in the mouse cortex.”11

The overall structure of the brain is consistent among fruit flies, based on the finding of “[a] high degree of stereotypy at every level; neuron counts are highly consistent between brains, as are connections above a certain weight.”12 This is consistent with previous research with different insect brains.13

Another finding from the research is that the fruit fly brain exhibits the characteristics of is what is called a “small-world network,” where the “nodes are highly clustered and path lengths are short.”14 Other examples of small-world networks are power grids, train routes, and electronic circuits. The brain of C. elegans was the first example identified of a small-world neural network. Characteristics of small-world networks include “enhanced signal-propagation, computational power, and synchronizability.”15 The key benefit for brain function is that it provides “highly effective global communication among neurons.”16

Overall, the research shows that the fruit fly brain has a high degree of complexity, but more importantly, much of it is specified complexity. This includes the engineering design of the various specialized neural networks and subnetworks. Some of the engineering design principles that are evident in aspects of the brain include optimization, efficiency, and coherence. As complex as the brain is shown to be so far from the research, it is likely even more complex than currently appears to be the case since the electrical connections have yet to be fully mapped in a similar way to the chemical connections

Rallying to the logic of design.

 Postcard from Venice: First Pan-European Conference on Intelligent Design

Gunter Bechly

Recently I had the great privilege and honor to attend a remarkable event in the beautiful and historic city of Venice, Italy. It was the first pan-European conference on intelligent design theory, organized by the Centro Italiano Intelligent Design (CIID), in collaboration with the foundation En Arche (Poland), BioCosmos (Norway), Centre for Intelligent Design (UK), Zentrum für BioKomplexität & NaturTeleologie (Austria), and Discovery Institute (USA). The conference was titled “Cosmos, Life, Intelligence, Information” and it was held at the prestigious and absolutely stunning venue of the Ateneo Veneto, which represents the oldest cultural institute still operative in Venice. The institute is dedicated to the spreading of science, education, and art and was officially founded in 1812, but originally dates back as far as 1458. It is situated in the historic center of Venice in a building from the early 1500s. The event was not advertised in advance and only included about 60 invited guests, to avoid any possible intervention by the Darwinist thought police, whose zealous activists already had prevented several such conferences at prestigious venues in the past.

The speakers came from all over Europe and America and addressed very different topics related to the question of intelligent design. After an introduction by the president of CIID, Carlo Alberto Cossano, the German physicist Professor Alfred Krabbe talked about “Fine-tuning in the universe,” which surprised me with some striking examples of fine-tuning in physics and astronomy that I had never heard of before. Professor Ferdinando Catalano elaborated on the strange relation between mathematics and physics in his talk “But does light ‘reflect’?”, and his Italian compatriot Professor Alessandro Giorgetti emphasized the extreme unlikelihood of the emergence of life from inanimate matter in his lecture about the “Origins of life and exobiology.”

Discontinuities in the Fossil Record

Next, I presented a talk about the “Scientific Challenges to Neo-Darwinism,” based on the discontinuities in the fossil record, the waiting time problem, the species pair challenge, and the incongruence of different lines of evidence in phylogenetics and molecular clock studies. Professor Steinar Thorvaldsen, an information scientist from Norway, talked about “Measuring the information in genes and DNA,” and Polish biologist Professor Stanisław Karpiński asked “Is the theory of evolution coherent or fragmentary?”, presenting fascinating new discoveries about communication and information processing in plants. British physician Dr. David Galloway introduced “The engineering of oxygen delivery in the newborn human” as another case of irreducibly complex systems. Last but not least, Dr. Casey Luskin from Discovery Institute gave an “Update on avenues of ID inspired research,” which showed the remarkable progress of intelligent design in the past years.

A Concluding Debate

The event concluded with a panel debate between theistic evolutionist Dr. Erkii Vesa Rope Kojonen (Finland) and ID proponent Casey Luskin about the compatibility of evolution and design. Both speakers are Christian theists, who agree that there is evidence for design in nature that cannot be sufficiently explained by blind forces of chance and necessity, but they differ in their views as to how and when the input of intelligent design happened. Rope Kojonen thinks that it was only at the very beginning of the universe, through a fine-tuning of the laws of nature and the initial conditions, while the development of life happened by mere Darwinian processes in this fine-tuned fitness landscape. On the other hand, Casey Luskin made a strong case for the necessity of ongoing activity of an intelligent designer during the history of life to explain complex adaptations and new proteins. While Rope Kojonen relied more on philosophical and theological arguments, Casey Luskin focused on the empirical scientific evidence and an inference to the best explanation, which in his and my humble opinion clearly favors intelligent design theory over theistic evolution. Nevertheless, it was very encouraging to see how such an exchange of different views can happen in a very respectful, charitable, and kind manner, very much unlike the aggressive attitude of many vocal ID critics on the Internet. After a discussion and Q&A session, the event ended with a wonderful dinner in an inspiring atmosphere of camaraderie and friendship.

All the talks were professionally recorded and will be made available on YouTube soon, and there are plans to publish English abstracts of the talks.

CIID should be congratulated for the excellent organization of this conference, which I hope will mark the beginning of more regular events like this in Europe to foster interdisciplinary exchange and advance the field of intelligent design research.

Quantity is trumping quality in science?

 

He shot at the king and didn't miss.

 

On the preservation of natural history.

 Fossil Friday: New Research on How Delicate Soft-Bodied Organisms Can Be Perfectly Preserved

Gunter Bechly

This Fossil Friday features the Cambrian arthropod Waptia fieldensis from the famous Burgess Shale. However, today we will not look into a particular fossil or group of organisms, but into the exceptional mode of fossil preservation of some of the oldest known animals from the Cambrian and the recently changed interpretation of how these fossil layers were formed. Paleontologists have generally assumed and postulated that perfect and complete preservation, especially of delicate soft-bodied organisms, suggests a gentle deposition in situ without significant transport that would certainly damage these fragile bodies. This view has been challenged by experimental studies that showed such organisms can remain entirely intact even when transported more than 20 km in turbulent sediment flows (Bath Enright et al. 2017). But how does this apply to real world fossil localities, especially the crucial sources for exquisitely preserved fossils of the first animals from the Cambrian Explosion? Two new studies have revised my views on two key localities, i.e., the Burgess Shale and the Emu Bay Shale.

Burgess Shale

The Burgess Shale, a world-renowned fossil site in the Canadian Rockies, provides one of the most complete windows into the Cambrian Explosion, a period about 508 million years ago when a remarkable diversity of complex life forms first appeared in the fossil record. Discovered in 1909 by paleontologist Charles Doolittle Walcott, the Burgess Shale is exceptional not only for its abundance of fossils but also for the extraordinary preservation of soft-bodied organisms, which are typically absent from the fossil record. This preservation includes fine details of tissues and appendages, capturing intricate anatomical features that illuminate the early history of animals. Scientific explanations for this unique preservation focus on taphonomy, the processes that affected these organisms from death to their fossilization, emphasizing the role of rapid burial and anoxic conditions.

According to the prevailing taphonomic model, the organisms in the Burgess Shale were buried quickly by underwater mudslides or turbidites, which were common in the deep marine environments where these creatures lived. These mudslides would have buried the organisms in a fine-grained, clay-rich matrix, isolating them from scavengers and decay. Furthermore, the water column above the burial site was likely low in oxygen, creating anoxic or dysoxic conditions that inhibited bacterial decomposition. This lack of oxygen, combined with rapid burial, allowed the soft tissues of these animals to be preserved in exquisite detail. Over time, mineral replacement of organic materials took place, particularly through carbon films that retained fine anatomical features. In some cases, other mineral replacements occurred, stabilizing the structures long enough for them to fossilize.

Further research emphasized the precise geochemical and sedimentological conditions that allowed for this unique preservation. Studies on clay mineralogy and trace metal concentrations in the Burgess Shale suggested that specific chemical interactions in the sediment helped to inhibit decay, possibly by creating an environment toxic to decay microbes. As a result, the Burgess Shale represents not only a key snapshot of Cambrian life but also an extraordinary example of the role that taphonomic processes play in determining what we see in the fossil record.

Thus, even the traditional view considered the Burgess Shale fossil assemblage as caused by catastrophic rapid burial. However, according to Bath Enright et al. (2017), “the exceptional preservation of organisms within the deposits has been used to argue that transport of these animals must have been minimal,” which those authors doubted based on their experiments. In a more recent follow-up study (Bath Enright et al. 2021), the same authors tested this with flume experiments to create analog flows and showed that transport of polychaete worms over tens of kilometers does not induce significant damage. They concluded “that the organisms of the Burgess Shale in the classic Walcott Quarry locality could have undergone substantial transport and may represent a conflation of more than one community.” Co-author Dr. Nic Minter commented in the press release by the University of Portsmouth (2021) that “this finding might surprise scientists or lead to them striking a more cautionary tone in how they interpret early marine ecosystems from half a billion years ago.” It goes without saying that this result of course also has important implications for our understanding of the over 40 known localities of the Burgess-Shale-Type (BST) preservation.

Emu Bay Shale

Such another BST locality is the Emu Bay Shale, located on Kangaroo Island in South Australia. It represents one of the most significant Cambrian fossil sites outside North America, providing valuable insights into the Cambrian Explosion, especially regarding arthropod diversity. Like the Burgess Shale, the Emu Bay Shale is remarkable for its exceptional preservation of soft tissues in fossils, including eyes, digestive tracts, and delicate appendages, which offer a detailed view of early animal anatomy. Dating to around 514 million years ago, it preserves a diverse array of Cambrian life forms, particularly trilobites and anomalocaridids, which are preserved with high fidelity, showing fine structures not typically fossilized.

Scientific views on the taphonomy of the Emu Bay Shale attributed its preservation quality to rapid burial and the local environmental conditions. Similar to the Burgess Shale, researchers suggested that the fossils were entombed quickly in fine-grained sediment, likely during submarine mudflows that swept organisms into deeper, oxygen-poor waters. Anoxic conditions in the burial environment would have slowed bacterial decay and minimized disruption by scavengers, while fine sediment encasement shielded delicate structures from mechanical breakdown. This unique combination of rapid burial and anoxia, possibly supplemented by specific chemical interactions in the sediment, allowed the Emu Bay Shale to capture fine anatomical details, adding a vital piece to our understanding of Cambrian ecosystems.

According to a brand new study by Gaines et al. (2024), published in the journal Science Advances, the Emu Bay Shale has to be newly interpreted. The authors document evidence for downslope mass transport of soft-bodied organisms in “density-driven sediment gravity flows” caused by “episodic high-energy events.” The press release explains that the sediments were “were catastrophically deposited into the ocean by debris flows,” which is “not where you would expect to see delicate, soft-bodied creatures preserved” (Gaines quoted in NSF 2024). The authors concluded that most taxa of the more than 25,000 fossils were transported and thus not buried in situ, which explains why “before these findings, the research community debated whether the Emu Bay Shale represented a shallow or deep environment” (NSF 2024).

Perfect Fossil Preservation Does Not Exclude Long Transport 

What makes the revised understanding of the taphonomy of these two key Cambrian localities very interesting is that the perfect preservation of the fossil from these localities is now considered to be consistent with a long transport in rough and turbulent sediment flows. Of course, this does not just apply to the Burgess Shale and Emu Bay Shale localities but can be extrapolated to numerous other “Konservat-Lagerstätten” with well-preserved marine and terrestrial fossils around the globe, such as the Devonian Hunsrück Shale in Germany and the Cretaceous Jehol biota in China (Bath Enright et al. 2017). A good example is the new study by O’Connell et al. (2024) about the terminal Ediacaran Nama biota, which showed that soft-bodied and biomineralizing organisms were transported in sediment gravity flows induced by storms and others events. The authors found that “nearly all soft-bodied and biomineralizing organisms preserved in the studied units were transported prior to final burial.” The authors also mention that “other work suggests that turbulent and transitional flows can transport soft-bodied organisms great distances with little damage (ca 20 km; Bath Enright et al., 2017, 2021).” 

Evolution is Neither a Fact nor Knowledge

These new interpretations show how quickly yesterday’s scientific textbook wisdom may be refuted as obsolete misinterpretation. In the strict sense of the notion of “knowledge” we do not know anything with certainty about the distant past. All we have is an ever-changing set of very preliminary and often weakly supported conjectures, combined with wild speculations and fancy storytelling, that more often than not later turn out to have been plausible but false. The famous philosopher of science Karl Popper cherished this procedure of “conjectures and refutations” as the very core of the scientific method. However, there is a fundamental difference between repeatable and observable law-like processes that can be mathematically modelled and empirically tested, and singular events in the past that can only be probabilistically inferred based on circumstantial evidence and certain assumptions. Earth history, paleobiology, and evolutionary biology are all historical “soft” sciences that cannot be considered as on an equal footing with experimental “hard” sciences like physics, chemistry, genetics, or physiology. Only the latter sciences provide us with all the benefits of modern medicine and technology. The historical sciences are basically ivory tower musings of hardly any practical value and dubious scientific status. Therefore, I consider the famous dictum of evolutionary biologist Theodosius Dobzhansky — that “nothing in biology makes sense except in the light of evolution” — as one of the biggest myths and blunders in modern science. On the contrary, all the just-so-stories of macroevolution are completely dispensable in all of real (experimental) biology. I would even suggest that “not much in biology makes sense except in the light of design,” which is why design language is so ubiquitous and indispensable even in the mainstream biosciences.

References

Bath Enright OG, Minter NJ & Sumner EJ 2017. Palaeoecological implications of the preservation potential of soft-bodied organisms in sediment-density flows: testing turbulent waters. Royal Society Open Science 4(6), 170–212. DOI: https://doi.org/10.1098/rsos.170212

Bath Enright OG, Minter NJ, Sumner EJ, Mángano MG & Buatois LA 2021. Flume experiments reveal flows in the Burgess Shale can sample and transport organisms across substantial distances. Communications Earth & Environment 2: 104, 1–6. DOI: https://doi.org/10.1038/s43247-021-00176-w

Gaines RR, García-Bellido DC, Jago JB, Myrow PM & Paterson JR 2024. The Emu Bay Shale: A unique early Cambrian Lagerstätte from a tectonically active basin, Science Advances 10(30): eadp2650, 1–9. DOI: https://doi.org/10.1126/sciadv.adp2650

NSF (National Science Foundation) 2024. A remarkable fossil assemblage gets a new interpretation. Phys.org October 30, 2024. https://phys.org/news/2024-10-remarkable-fossil-assemblage.html

O’Connell B, McMahon WJ, Nduutepo A, Pokolo P, Mocke H, McMahon S, Boddy CE & Liu AG 2024. Transport of ‘Nama’-type biota in sediment gravity and combined flows: Implications for terminal Ediacaran palaeoecology. Sedimentology early view, 1–43. DOI: https://doi.org/10.1111/sed.13239

University of Portsmouth 2021. Fossil secret may shed light on the diversity of Earth’s first animals. Phys.org June 2, 2021. https://phys.org/news/2021-06-fossil-secret-diversity-earth-animals.html