Primeval tech not letting up vs. Darwinism

 Irreducibly Complex, Bacterial Cell Wall Manufacture Is an Evolutionary Enigma

Jonathan McLatchie

One of the most incredible features of cellular life is the capability of self-replication. Bacterial cells divide by a process known as binary fission — an amazing feat of engineering, requiring a myriad of different proteins. Several features of bacterial cell division exhibit irreducible complexity. This represents a fundamental challenge to evolutionary explanations of its origins, since a precondition of natural selection is differential survival, and self-replication is itself required for differential survival. Thus, one cannot plausibly appeal to natural selection to explain the origins of bacterial cell division without assuming the existence of the very thing one is attempting to explain. Here, I will focus only on the severing and re-synthesis of the bacterial cell wall.

The Breaking and Manufacture of the Cell Wall

The peptidoglycan cell wall is a rigid structure that surrounds and protects the bacterium, conferring upon the cell structural integrity and shape. As a bacterial cell divides, its cell wall must grow as the cell elongates in preparation for division. In rod-shaped bacteria, this takes place at multiple locations along the cell, whereas in coccus-shaped bacteria, the cell wall grows outward from the FtsZ ring in opposite directions.1 Cell wall growth requires the controlled cleavage of the existing peptidoglycan layer. The β-1,4 glycosidic bonds that link N-acetylglucosamine and N-acetylmuramic acid are hydrolyzed by enzymes called autolysins, which have to be very carefully regulated because they can result in programmed cell death.2,3 Specific regulatory mechanisms guide the localization of autolysins to the site of cell division.4,5,6 These regulatory mechanisms ensure that autolysins are targeted only to the appropriate region of the cell. Autolysins bind to the peptidoglycan at the site of cell division, and catalyze the hydrolysis of the peptide cross-links within the cell wall. This cleavage weakens the peptidoglycan at the division site, allowing the cell wall to undergo controlled breakage. The gaps are then filled in with additional cell wall material.

          The first stage of re-synthesis of the cell wall is the formation of the peptidoglycan precursors.7 A chain of five amino acids (a pentapeptide) is added to N-acetylmuramic acid.8 N-acetylglucosamine is subsequently attached to the end of the N-acetylmuramic acid. The result is a peptidoglycan precursor. An extremely hydrophobic molecule, called bactoprenol, is embedded in the inner cytoplasmic membrane.9,10 Bactoprenol shuttles the hydrophilic peptidoglycan precursors from the inner side of the membrane, where they are synthesized, to the outer side of the membrane where they are needed for the assembly of the cell wall. This hydrophobic protein is essential because the hydrophilic precursors cannot easily traverse the hydrophobic membrane on their own.

Once bactoprenol reaches the periplasmic space (in gram-negative bacteria) or the cell exterior (in gram-positive bacteria), it transfers the peptidoglycan precursors to the peptidoglycan assembly site. There, glycosyltransferases and penicillin-binding proteins (also called transpeptidases) utilize these precursors to build the glycan chains and cross-link them to provide the cell wall with stability and strength.11,12 The penicillin-binding proteins are responsible for catalyzing the cross-linking of the peptide side chains between diaminopimelic acid and D-alanine on adjacent peptides. In gram-positive bacteria, cross-links typically occur from an L-lysine to a D-alanine of adjacent peptides. At the end of the peptidoglycan precursor, there exist initially two D-alanine residues, but one is removed during the reaction leaving one in the final molecule. In E. coli a specialized penicillin-binding protein called FtsI is the key player in transpeptidation at the septum.13 Localization of FtsI to the septum itself requires an intact N-terminal membrane anchor in addition to the division proteins FtsZ, FtsA, FtsQ, FtsW, and FtsL.14,15

An Evolutionary Enigma

What about this process is a challenge to evolution? Absolutely critical to cell division in virtually all bacteria is the ability to re-synthesize peptidoglycan. How do we know it is so crucial? The mechanism of action of beta-lactam antibiotics (including penicillin, cephalosporins, and monobactams) is to interfere with the peptidoglycan cross-linking.16,17 As their name implies, penicillin-binding proteins are the target of penicillin, which causes them to lose their enzymatic activity. The activity of the autolysins weakens the cell wall to such an extent that the cell lyses (bursts open). Some other, non beta-lactam, antibiotics (e.g., lactivicins) have a similar mechanism of action.18,19 Antibiotics may also target cell wall precursors. For instance, the antibiotic nisin associates with cell wall precursor lipid II and locks it in a stable complex, thereby effectively inhibiting the peptidoglycan synthesis cycle.20,21

Consider the following two observations: 

Critical to the elongation process is the severing of the peptidoglycan cell wall by the autolysins. 

Critical to cell viability is the re-synthesis of the peptidoglycan cell wall. 

These processes have to be highly coordinated. If the mechanism for severing the cell wall arose without simultaneously having a mechanism in hand to rebuild the cell wall, the cell would not survive the division process. Both mechanisms must arise together. One might object that a mechanism for repairing breaks in the cell wall could have arisen first, before being coopted into the cell division machinery. But without being able to sever the cell wall, there could be no division and thus no differential survival, and by extension no natural selection.

This process of severing and rebuilding the cell wall is critical to cell division in almost all bacteria. A notable exception is species belonging to the genus Mycoplasma, which lack a cell wall. But this has little relevance to accounting for the origins of the mechanisms of severing and rebuilding the peptidoglycan in those species that dopossess a cell wall. As soon as the cell wall — which is a rigid outer layer that provides structural support to the cell — arose, there would need to be a mechanism for re-modelling and splitting it to allow the bacterium to divide into two daughter cells. Moreover, Mycoplasma species are obligate parasites, dwelling in osmotically protected habitats. Furthermore, in place of a cell wall they typically have sterols in their cytoplasmic membrane, which imparts to them greater rigidity and strength.

Foresight Is Required, Pointing to Intelligent Design

In summary, cell wall remodeling and splitting, essential to the cell division process in bacteria, is irreducibly complex, requiring both the mechanism for severing the peptidoglycan and the resynthesis process to arise simultaneously. Without being able to rebuild the cell wall, the cell will burst due to the osmotic pressure. But without being able to sever the peptidoglycan, the cell cannot divide. Evolutionary processes cannot select for some future utility that is only realized after passing through a maladaptive intermediate. This phenomenon therefore requires foresight, and is thus much more probable on the hypothesis of design than it is on mindless chance and necessity.

Notes

Margolin W. Sculpting the bacterial cell. Curr Biol. 2009 Sep 15;19(17):R812-22.

Zoll S, Pätzold B, Schlag M, Götz F, Kalbacher H, Stehle T. Structural basis of cell wall cleavage by a staphylococcal autolysin. PLoS Pathog. 2010 Mar 12;6(3):e1000807.

Mitchell SJ, Verma D, Griswold KE, Bailey-Kellogg C. Building blocks and blueprints for bacterial autolysins. PLoS Comput Biol. 2021 Apr 1;17(4):e1008889.

Zielińska A, Billini M, Möll A, Kremer K, Briegel A, Izquierdo Martinez A, Jensen GJ, Thanbichler M. LytM factors affect the recruitment of autolysins to the cell division site in Caulobacter crescentus. Mol Microbiol. 2017 Nov;106(3):419-438.

Mueller EA, Iken AG, Ali Öztürk M, Winkle M, Schmitz M, Vollmer W, Di Ventura B, Levin PA. The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment. Mol Microbiol. 2021 Jul;116(1):311-328.

Schlag M, Biswas R, Krismer B, Kohler T, Zoll S, Yu W, Schwarz H, Peschel A, Götz F. Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl. Mol Microbiol. 2010 Feb;75(4):864-73.

        Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus. 2021 Jan;9(2).

Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. 1972 Dec;36(4):407-77.

Thorne KJ, Kodicek E. The structure of bactoprenol, a lipid formed by lactobacilli from mevalonic acid. Biochem J. 1966 Apr;99(1):123-7.

Barker DC, Thorne KJ. Spheroplasts of Lactobacillus casei and the cellular distribution of bactoprenol. J Cell Sci. 1970 Nov;7(3):755-85.

Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev. 2008 Mar;32(2):234-58. doi: 10.1111/j.1574-6976.2008.00105.x. Epub 2008 Feb 11. Erratum in: FEMS Microbiol Rev. 2008 May;32(3):556.

Sauvage E, Terrak M. Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials. Antibiotics (Basel). 2016 Feb 17;5(1):12

       Wissel MC, Weiss DS. Genetic analysis of the cell division protein FtsI (PBP3): amino acid substitutions that impair septal localization of FtsI and recruitment of FtsN. J Bacteriol. 2004 Jan;186(2):490-502.

Mercer KL, Weiss DS. The Escherichia coli cell division protein FtsW is required to recruit its cognate transpeptidase, FtsI (PBP3), to the division site. J Bacteriol. 2002 Feb;184(4):904-12.

Weiss DS, Chen JC, Ghigo JM, Boyd D, Beckwith J. Localization of FtsI (PBP3) to the septal ring requires its membrane anchor, the Z ring, FtsA, FtsQ, and FtsL. J Bacteriol. 1999 Jan;181(2):508-20.

Beadle BM, Nicholas RA, Shoichet BK. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation. Protein Sci. 2001 Jun;10(6):1254-9.

Mora-Ochomogo M, Lohans CT. β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates. RSC Med Chem. 2021 Aug 4;12(10):1623-1639.

Nozaki Y, Katayama N, Harada S, Ono H, Okazaki H. Lactivicin, a naturally occurring non-beta-lactam antibiotic having beta-lactam-like action: biological activities and mode of action. J Antibiot (Tokyo). 1989 Jan;42(1):84-93.

             Brown T Jr, Charlier P, Herman R, Schofield CJ, Sauvage E. Structural basis for the interaction of lactivicins with serine beta-lactamases. J Med Chem. 2010 Aug 12;53(15):5890-4.

Müller A, Ulm H, Reder-Christ K, Sahl HG, Schneider T. Interaction of type A lantibiotics with undecaprenol-bound cell envelope precursors. Microb Drug Resist. 2012 Jun;18(3):261-70.

Münch D, Müller A, Schneider T, Kohl B, Wenzel M, Bandow JE, Maffioli S, Sosio M, Donadio S, Wimmer R, Sahl HG. The lantibiotic NAI-107 binds to bactoprenol-bound cell wall precursors and impairs membrane functions. J Biol Chem. 2014 Apr 25;289(17):12063-12076.

Design on the wing.

 Appreciating Bird Mimicry and the Other Exceptional, Designed Talents

David Coppedge

From the hummingbird with its nectar-trap tongue, to starlings in formation flight, to Arctic terns in long-distance migration, it would take a book of Evolution News articles even to begin to do justice to the many diverse kinds of birds that warrant our admiration. From time to time we can, though, point out particular cases that have come to light in scientific research.

Image Stabilization

Lovebirds; aren’t they sweet. We’re not talking about newlyweds, but small parrots that inhabit Africa and Madagascar (which do, by the way, show affectionate behavior). A zoologist incorporated the help of mechanical engineers to study something Olympic about them: they can turn their heads “super-fast” in flight (pictured above). In a paper in PLOS ONE, the team measured the head turn rate. Although the birds flick their heads back and forth, the rotational motion measured by a high-speed camera is exceptionally fast: 2700 degrees per second. 

High-speed flight recordings revealed that rapidly turning lovebirds perform a remarkable stereotypical gaze behavior with peak saccadic head turns up to 2700 degrees per second, as fast as insects, enabled by fast neck muscles. In between saccades, gaze orientation is held constant. By comparing saccade and wingbeat phase, we find that these super-fast saccades are coordinated with the downstroke when the lateral visual field is occluded by the wings. Lovebirds thus maximize visual perception by overlying behaviors that impair vision, which helps coordinate maneuvers…. Our observations show that rapidly maneuvering birds use precisely timed stereotypic gaze behaviors consisting of rapid head turns and frontal feature stabilization, which facilitates optical flow based flight control.

The strategy resembles the way early combat aircraft could fire machine-gun rounds without blowing off the propellers. The bird turns the head just in time to minimize the time the wing is in the way of seeing. A summary of the findings at Phys.org gives another reason why this research is interesting. “The authors also hope that the accuracy and speed of these visually guided flight-maneuvers may inspire camera rotation design in drones to improve imaging.” 

Lest you feel any sense of inferiority at this little bird’s design, notice what the authors write in the Abstract: “Similar gaze behaviors have been reported for visually navigating humans.” This paper in Current Biology about “microsaccades” (tiny eye movements), which unwittingly sample our visual field during focused attention, also bears reading (see the summary at Medical Xpress).

Smell Navigation

The ability to navigate by the sense of smell or by the Earth’s magnetic field is widespread in many types of animals. Here’s a case in point: seabirds. An article at Live Science reports on work by zoologists in the UK who found that “Seabirds smell their way home.” Flying over large expanses of open water, birds like Cory’s shearwaters manage to find their nesting sites and feeding grounds without error. How do they do it? There aren’t many cues available. The authors ruled out some senses, like sound.

Observing how the birds explore an area in detail then move a distance and repeat (a search strategy called a Lévy flight pattern), the researchers found that models based on the sense of smell gave the best fit. It’s not easy, though. For smell navigation to work, not only must the sense of smell be incredibly acute, but the birds have to be able to integrate olfactory data with other forces in the environment.

Birds may associate smells, such as those from phytoplankton, with wind directions, the researchers noted. For instance, the seabirds may know to fly westward when they smell one odor and to fly eastward when they smell another. Or, a combination of both smells may prompt them to fly northeast, the researchers said.

However, smells aren’t always detectible because of atmospheric turbulence, so birds will reorient and change direction until they find another recognizable smell, the researchers found.

In addition, the birds must have an “odor map” written in the brain that associates the odor cues with memory. In effect, the cues tell the bird, “This combination of odors means you are here, and you need to head that way.” As the feeding ground approaches, the birds can rely on additional cues, like “landmarks, flights of other birds and ‘colony odors’.” Some fish, including salmon, have a similar capability: a nasal switchboard that guides them through a maze of tributaries to its natal stream.

Vocal Imitation

Who hasn’t had fun listening to parrots imitate human speech? It takes a special kind of brain to do this. Parrots, parakeets (budgerigars), cockatiels, keas, and our affectionate friends the lovebirds are good at it. Neurologists at Duke University were curious to know what structures in the brain seem to be responsible. They found particular regions they dubbed “shells” around core speech centers that are found in all these species. One researcher’s reaction has some bearing on Kuhnian science:

“The first thing that surprised me when Mukta and I were looking at the new results is, ‘Wow, how did I miss this all these years? How did everybody else miss this all these years?’” said Jarvis, who is also member of the Duke Institute for Brain Sciences. “The surprise to me was more about human psychology and what we look for and how biased we are in what we look for. Once you see it, it’s obvious. I have these brain sections from 15 years ago, and now I can see it.” 

The news release seems obsessed with how this brain region evolved, stating that whatever mutation led to it happened 29 million years ago, based on assumed evolutionary lineages. That doesn’t come close to explaining it:

The new results support the group’s hypothesis that in humans and other song-learning animals, the ability to imitate arose by brain pathway duplication. How such a copy-and-paste job could have happened is still unknown.

It’s not clear how duplicating a gene or pathway can cause a new complex ability like voice imitation: “It takes significant brain power to process auditory information and produce the movements necessary for mimicking sounds of another species,” one of the researchers said. The article does not speculate on what kind of mutational event led to the exceptional abilities of unrelated birds, like the mockingbird or lyrebird.

Let the reader enjoy the 350+ word vocabulary of Clover, alleged to be the best talking parrot in the world. 

But of what evolutionary survival value is this ability? Clover seems to be enjoying her intricate brain and vocal apparatus. If we don’t think human impressionists evolved their repertoire by mistake, perhaps we should give intelligent design, not Darwinian evolution, the credit for bird mimicry and the other exceptional talents.

Still continuing to rethink the unrethinkable.

 

Cocaine shark?

 

Science as servant vs. science as master.

 Science for Insight or Science for Power?

Peter Biles

“Should machines replace mathematicians?” That’s the headline of a new post by science writer John Horgan, who comments on the current state of mathematics and the growing potential of AI and computers to do all the “heavy lifting” in the mathematical enterprise. Horgan notes that mathematicians were the ones to develop computers in the first place, but now, with the advent of advanced computing and artificial intelligence, the role of human-driven mathematics is getting to be less certain. However, maybe math is not only about input and output but a “way of being human.” For Horgan, data and computation don’t get to the heart of scientific and mathematical endeavors. It needs to mean something more than an impersonal process geared towards calculable ends. 

Science’s Core Purpose

Horgan not only talks about math in his article. He also relates the discussion to the core purpose of science. Science, in one definition, means gaining insights into nature. However, in today’s utilitarian society, science is less about contemplating the beauty of nature and more about securing power over nature for the sake of our ease, convenience, and control. He writes, 

We value science for its applications, too. Sentimental science writing, including mine, implies that science’s purpose is insight into nature. In the modern era, however, science’s primary goal is power. Science helps us manipulate nature for various ends: to extend our lives, to enrich and entertain us, to boost the economy, to defeat our enemies. Modern physics, to most of us, is unintelligible, but who cares when physics gives us smartphones and hydrogen bombs?

JOHN HORGAN, SHOULD MACHINES REPLACE MATHEMATICIANS? — JOHN HORGAN (THE SCIENCE WRITER)

Science and Magic

The comment reminds me of a famous observation by C. S. Lewis, who wrote in The Abolition of Man:

There is something which unites magic and applied science while separating both from the wisdom of earlier ages. For the wise men of old the cardinal problem had been how to conform the soul to reality, and the solution had been knowledge, self-discipline, and virtue. For magic and applied science alike the problem is how to subdue reality to the wishes of men.

It sounds strange to equate “applied science” (i.e., technology) with magic, but doing so reveals the potential of using scientific knowledge merely as a means to power instead of as a source of “insight,” as Horgan writes.

No intelligence allowed?

 

On the relevance of God.

 

The Iranian revolution: an exploration.

 

The West's destiny : not so manifest after all?

 

On making a killing doing those dirty jobs that need doing.

 

On Korea's Poland syndrome?

 

Machiavelli: a brief history.

 

How to not get taken for a ride re:your next car deal.

 

Trinitarian theology : gateway drug to Unitarian Christianity?

 

Nuking the carbon issue?

 

Primeval tech trolling Darwinism continued.

 Cell Vesicles Wear Sophisticated Coats, Defying Unguided Evolutionary Explanations

 David Coppedge

Envision a day when self-driving cars make driving obsolete. Now, imagine a far-future day when you don’t even have to get in the car. Instead, as you walk out the front door, a car assembles around you, lifts off the ground, floats you to your destination, then disassembles in anticipation of picking up the next passenger. Something like this actually happens in living cells. According to news from the European Molecular Biology Laboratory (EMBL):

Researchers at EMBL Heidelberg have produced detailed images of the intricate protein-coats that surround trafficking vesicles — the “transport pods” that move material around within biological cells. The study, published today in Science, provides a new understanding of the complex machines that make up the cells’ logistics network.

Vesicles are responsible for transporting molecules between the different compartments within a cell and also for bringing material into cells from outside. There are several types of vesicle: each has a specific type of coat which is made up of different proteins and assembles onto a membrane surrounding the vesicle.

There are three models of “transport pods” that molecular biologists know about, each with its own specific coat proteins: Coat Protein 1 (COPI), Coat Protein 2 (COPII), and clathrin-coated vesicle (CCV). Each coat has its own proteins, adaptors, and functions. The paper in Science looks in detail at COPI; but first, let’s mention COPII. This type of vesicle takes proteins from the endoplasmic reticulum (ER), where they were assembled, to the Golgi apparatus where they will be packaged for delivery. This is called anterograde (forward) transport.

COPI is the reverse; it takes proteins from the Golgi back to the ER, or to different compartments of the Golgi. This is called retrograde (backward) transport. Surprisingly, the coat proteins on these vesicles are very different. COPII coats are made of four proteins that assemble with four-fold symmetry in a sequential manner, using separate adaptor proteins. COPI is more complicated. It has seven discrete proteins that come together simultaneously, forming complexes with triangular symmetry that include the adaptor function (i.e., allowing the complex to attach to the vesicle membrane).

Pushing the Envelope

The EMBL researchers pushed the envelope of cryoelectron microscopy to determine the nature of the “triads” called coatomers that make up the coat. They found that the seven proteins form two complexes that overlap into a layer 14 nanometers (nm) thick — a substantial fraction of the typical 100-nm-diameter vesicle. A Perspective article in the same issue of Science says there’s still a lot to learn about these coats: “it remains to be determined what specific roles these conformations play in the respective coat functions,” Noble and Stagg write. What is known is that the coatomer triads make contact with up to four neighboring triads. This gives them structural flexibility that is distinct from the other coated vesicle types. The authors of the paper speculate about the reasons for this:

In existing models for clathrin and COPII vesicle coats, multiple identical subunits each make the same set of interactions with the same number of neighbors. Structural flexibility allows formation of vesicles from different total numbers of subunits. Based on these principles, both clathrin-like and COPII-like models have been proposed for the assembled COPI coat. We found instead that assembled coatomer can adopt different conformations to interact with different numbers of neighbors. By regulating the relative frequencies of different triad patterns in the COPI coat during assembly — for example, by stabilizing particular coatomer conformations — the cell would have a mechanism to adapt vesicle size and shape to cargoes of different sizes. 

The paper includes color models and two motion animations of how the proteins fit together, protecting the cargo as it rides to its destination from organelle to organelle.

Clathrin Coats

A better-understood protein coat is made of clathrin. The name comes from a Latin word for lattice. Individual clathrin molecules, made of three heavy chains and three light chains, look like a three-spoked pinwheel called a triskelion. They fit together beautifully around the vesicle into a cage-like structure that resembles a geodesic dome. A beautiful Animation from Harvard Medical School shows how numerous other proteins work with clathrin to form the vesicle coat and disassemble it after use, so the triskelia can be recycled. The vesicles can import and export molecules to the exterior of the cell or transport them within the cytoplasm. Clathrin proteins are also implicated in cell division, where they assist in arranging chromosomes on the spindle.

In Need of an Update

The animation will require an update, though, because something new was reported about clathrin-coated vesicles (CCV) and the pits (CCP) that form when the membrane invaginates to bring cargo in from outside. Another EMBL team, also reporting in Science, found that clathrin is more gymnastic than previously recognized. 

Unlike as shown in the animation, the clathrin lattice forms flat on the inner membrane surface before invagination begins. Then, as the membrane folds inward, the lattice stretches and reconfigures itself, maintaining the same surface area but following the shape of the vesicle as it elongates. With its cargo safely inside, the vesicle pinches off and forms a sphere. The news from EMBL expresses surprise at the shape changes:

John Briggs, senior scientist at EMBL Heidelberg, said: “Our results were surprising, because the proteins have to undergo some complicated geometric transformationsto go from a flat to a curved shape, which is why the second model was favoured by scientists for such a long time.”

(The “second model”, now falsified, refers to the idea that “clathrin assembles directly, assuming the shape of the membrane as it is drawn inwards.”) The paper describes how the growing cage must change its geodesic structure as the vesicle forms: 

In order to bend, flat lattices composed primarily of hexagons must acquire pentagons requiring extensive molecular rearrangements and removal of triskelia.

Why would the cell perform this more difficult gymnastic routine? The final paragraph offers some possible reasons:

Recruitment of clathrin before membrane bending provides a flat, dynamic array as a platform for cargo recruitment. This implies that the membrane to be internalized and the size of the future vesicle are not determined by clathrin geometry during assembly into a curved cage but rather are selected before invagination during cargo recruitment. Rapid clathrin exchange is consistent with a dynamically unstable lattice — dynamic instability is a common property within networks of low-affinity protein interactions. It would allow for stochastic abortion of sites that initiate but fail to cross a growth- or cargo-mediated checkpoint before investing energy in membrane bending. During invagination, further exchange would allow clathrin reorganization and bending of the lattice into a defined cage that requires active disassembly.

One thing not mentioned in the articles is the rapidity of vesicle formation and disassembly. Suffice it to say that clathrin-coated endocytosis and exocytosis occur at the tips of nerve cells, where electrical signals must cross synapses. The vesicles form at one nerve, cross the synapse carrying the cargo, and are taken in by the next nerve cell in line. How long does it take your brain to feel pain from a stubbed toe? A lot of CCVs formed, crossed synapses, and disassembled in that very quick response!

Evolution or Design?

As usual, the articles and papers say very little about evolution. If mentioned at all, it was about the lack of evolution: e.g., “The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human.” Only the Perspective piece by Noble and Stagg ventures further: 

Individual proteins in the three different coat protein complexes share similar folds and are proposed to be distant evolutionary relatives. Despite these similarities, the coats have evolved different functional mechanisms….

One possibility is that the proto-COPI coat evolved the four different linkages to expand the repertoire of geometries that the coat can accommodate and thus adapt to the secretory needs of the cell.

These suggestions amount to little more than after-the-fact assertions of evolutionary belief. One cannot invoke a blind, unguided process to say that it “evolved to” meet the needs of the cell. Darwinian natural selection has no foresight.

The complexity of these coats, and the accessory proteins that build them, attach them to vesicles, and disassemble them, defy unguided evolutionary explanations. They exhibit irreducible complexity; they don’t work unless all the protein parts are present simultaneously. They exhibit beauty in the way they organize into geometric shapes. The shapes, in turn, are dictated by digital codes in the genome that produce sequences that fold into building blocks. These building blocks, like the triskelion of clathrin, have no knowledge of the elegant geodesic domes that they will be fitted into. The triskelia are also blind to their attachment points that will be used by two other proteins that will disassemble the vesicle. 

We see only glimpses of structures we don’t yet fully understand. Why are separate coats needed for the three types of transport? What types of vesicles need the different coats? What specific advantages do the different coats provide for transport in one direction and not the other? What molecules need coated vesicles as opposed to uncoated vesicles? What function does each protein in the coat provide? 

Further research at higher resolution will undoubtedly yield more knowledge about vesicular transport. One thing is clear so far; the elegance of these systems, their ability to reshape their geometry as they grow, their adaptability to cargoes of many sizes, the rapidity of their action, and their conservation from yeast to humans all proclaim, “Intelligent design!”

The brain :Jack of all trades

 How Can a Woman Missing Her Olfactory Bulbs Still Smell?

Denyse O Leary

Even since neuroscientists started imaging the brain, they’ve been turning up cases where people are missing brain parts we would expect them to need in order to do something — but they are doing that very thing anyway. One example, written up in Live Science in 2019, concerns women who are missing their olfactory bulbs but can still smell.

Researchers have discovered a small group of people that seem to defy medical science: They can smell despite lacking “olfactory bulbs,” the region in the front of the brain that processes information about smells from the nose. It’s not clear how they are able to do this, but the findings suggest that the human brain may have a greater ability to adapt than previously thought.

YASEMIN SAPLAKOGLU, “WOMEN MISSING BRAIN’S OLFACTORY BULBS CAN STILL SMELL, PUZZLING SCIENTISTS,” LIVESCIENCE,NOVEMBER 6, 2019. THE PAPER IN NEURON IS OPEN ACCESS.

All the More Remarkable

The story is all the more remarkable when we consider that her sense of smell was especially good; that was why she had signed up for the Israeli researchers’ study. Deciding to pursue the matter, the researchers tested other women. On the ninth try, they found another left-handed woman who could smell without an olfactory bulb.

A researcher who was not involved in the study, Joel Mainland of the Monell Chemical Senses Center in Philadelphia, was asked for comment:

The findings are “pretty counter to most of what the field thinks,” Mainland told Live Science. “I think it’s pretty critical that we figure out what’s happening.”

Yes. But that could take a while because there are a number of similar situations out there.

Last year, Medical Express reported on a woman who lacked a left temporal lobe, believed to be the language area of the brain:

EG told Fedorenko and her team that she only came to realize she had an unusual brain by accident—her brain was scanned in 1987 for an unrelated reason. Prior to the scan she had no idea she was different. By all accounts she behaved normally and had even earned an advanced degree. She also excelled in languages — she speaks fluent Russian — which is all the more surprising considering the left temporal lobe is the part of the brain most often associated with language processing.

Eager to learn more about the woman and her brain, the researchers accepted her into a study that involved capturing images of her brain using an fMRI machine while she was engaged in various activities, such as language processing and math. In so doing, they found no evidence of language processing happening in the left part of her brain; it was all happening in the right. They found that it was likely the woman had lost her left temporal lobe as a child, probably due to a stroke. The area where it had been had become filled with cerebrospinal fluid. To compensate, her brain had developed a language network in the right side of her brain that allowed her to communicate normally. The researchers also learned that EG had a sister who was missing her right temporal lobe, and who also had no symptoms of brain dysfunction — an indication, the researchers suggest, that there is a genetic component to the stroke and recovery process in the two women.

BOB YIRKA, “WOMAN WITH NO LEFT TEMPORAL LOBE DEVELOPED A LANGUAGE NETWORK IN THE RIGHT SIDE OF HER BRAIN,” MEDICAL XPRESS,APRIL 14, 2022 THE PAPER IS OPEN ACCESS.

It’s also come out that one in 4000 people lacks a corpus callosum. That’s the structure of neural fibers that transfers information between the brain’s two hemispheres. It would seem a pretty important part pf the brain yet 25 percent of those who lack it show no symptoms. The others suffer mild to severe cognitive disorders. But we may well wonder how people manage in this situation at all:

In a study published in the journal Cerebral Cortex, neuroscientists from the University of Geneva (UNIGE) discovered that when the neuronal fibres that act as a bridge between the hemispheres are missing, the brain reorganises itself and creates an impressive number of connections inside each hemisphere. These create more intra-hemispheric connections than in a healthy brain, indicating that plasticity mechanisms are involved. It is thought that these mechanisms enable the brain to compensate for the losses by recreating connections to other brain regions using alternative neural pathways.

UNIVERSITÉ DE GENÈVE, “A MALFORMATION ILLUSTRATES THE INCREDIBLE PLASTICITY OF THE BRAIN,” SCIENCEDAILY, OCTOBER 30, 2020. THE PAPER IS OPEN ACCESS.

Prior to Brain Imaging

Recall that, prior to brain imaging, so long as a person was functioning normally, no one had any reason to suppose that a key brain part might simply be missing. And, let’s say its absence was discovered at autopsy. Who is to say that the absence of that part didn’t play some role in bringing about the person’s death? So it was only in recent decades that researchers discovered people of normal abilities with absent brain parts. That’s probably why we hear expressions like “seem to defy medical science” and “incredible plasticity” from the science media now.

Neuroplasticity is perhaps best understood as the human mind reaching out past physical gaps and barriers in any number of inventive ways. And it raises a question: If the mind is merely what the brain does, as many materialist pundits claim, what is the mind when the brain … doesn’t? At times, the mind appears to be picking up where the brain left off. 

Michael Egnor and I are looking forward to tackling topics like that in The Human Soul (Worthy, 2025).

Stateless monopolies vs. democracy?

 

Against censorship?

 

Tom Sowell educates re:education

 

The fossil record continues to set Darwinism straight.

 Fossil Friday: Eozoön, the Dawn Animal Fallen from Grace

Gunter Bechly

In the late 1850s the Canadian geologist William Logan, who as director of the Geological Survey of Canada mapped the geology of the country and authored the monumental Geology of Canada, discovered striped rocks from Precambrian limestone of eastern Canada, which he believed to be fossils of early life forms. He announced the discovery 1864 at a conference in Great Britain (Logan 1864, 1865), which immediately attracted tremendous interest and strong support by the British protistologist William Benjamin Carpenter. Famous geologist Charles Lyell commented that this represents “one of the greatest geological discoveries of my time” (Lyell 1864). Logan sent samples to his Canadian colleague John William Dawson (1865), who described the material as giant fossil protists, which he named Eozoön canadense, the dawn animal from Canada (also see Dana 1865). Dawson called it “one of the brightest gems in the scientific crown of the Geological Survey of Canada,” because at this time it was the earliest known evidence for life on Earth and “created a sensation in the geological community” (Adelman 2007).

Meet the Eozoönists

Most contemporary scientists did not doubt that Eozoön is a genuine fossil organism, with the exceptions of geologist William King and chemist Thomas Rowney from Queen’s College. These two skeptics, who did not believe in a biological origin of Eozoön, published a critique just a year after the original description and initiated one of the greatest scientific controversies of the 19th century. The supporters of the authenticity of the fossils, led by Dawson and Carpenter (1865), were called the Eozoönists, and both sides heavily relied on the scientific authority of their proponents and disputed the credibility of their opponents (Adelman 2007, O’Connor 2023). German naturalist Otto Hahn (1876) supported the critical view of King and Rowney with a paper refuting the fossil status of Eozoön. Other critics were the British protistologist Henry Carter (1874a, 1874b, 1874c) and the German zoologist Karl Möbius (1878), who both disputed any relationship with known protists, as well as the British geologist Henry Johnston-Lavis, who described very similar structures from volcanic marble shot out of Mount Vesuvius in Italy (Johnston Lavis & Gregory 1894), which were clearly of inorganic origin and therefore considered by many as final nail in the coffin of Eozoön. Nevertheless, the controversy persisted, and as late as 1947 Eozoön was endorsed as a first life form in a high school biology textbook (Moon et al. 1947). Since the 1950s other supposed evidence for Precambrian life began to accumulate (Schopf 2000), so that Eozoön simply lost its crucial importance for a solution to Darwin’s most vexing problem of a “missing Precambrian history of life” (also see Stephen C. Meyer’s 2013 book Darwin’s Doubt).

The Rise and Fall of Eozoön

Several papers in the past decades reviewed the scientific history of the rise and fall of Eozoön (O’Brien 1970, Schopf 2000, Adelman 2007, Wilson 2011, Dolan 2023, O’Connor 2023). Dolan (2023) recently showed that Eozoön “was never indisputably proven to be inorganic. Rather Eozoön simply faded away after its most ardent defenders died … To paraphrase a quote attributed to Mark Twain, the rumor of the death of Eozoön, announced with some authority at least three times, was each time, an exaggeration. King and Rowney believed that they had disproved the organic nature of Eozoön in 1866. Some 13 years later, Mobius clearly felt he had to show that Eozoön was not a fossil forminifera, as did Johnston-Lavis when he announced his discovery of Eozoön structures in volcanic ejecta in 1894.” 

Of course, there was a deeper reason why most scientists of Darwin’s era preferred to strongly defend Eozoön. This reason was clearly formulated by O’Brien (1970) in his review of the case:

… every aspect of nineteenth-century paleontology was scrutinized for its bearing on evolution …

There were two chief reasons for the persistence of the dispute. Most obvious and most important was the inability of early paleontology to settle the matter. The second reason, seldom stated by the disputants, was the significance of Eozoön in the larger issue of derivation of species. For, were Eozoön proved to be organic, evolutionists would be confronted with the most impressive of all gaps in the paleontological record, a gap that would give pause to even the most ardent evolutionist. On the other hand, if this gap were successfully explained or overcome by the finding of subsequent forms related to Eozoön, the evolutionists could rejoice in having found, at the earliest date of known animal life, the simplest form of life, a form reasonably akin to the “one primordial form” of Darwin’s speculation. In short, there was something at stake for both sides in the greater scientific controversy.

Darwin himself was interested in Eozoön and its promise for his position. He introduced Eozoön into the fourth edition of The Origin of Species: “After reading Dr. Carpenter’s description of this remarkable fossil, it is impossible to feel any doubt regarding its organic nature.” Darwin cited Eozoön in his famous tenth chapter, “On the Imperfection of the Geological Record,” as an indication that gaps in the paleontological record were being filled, and that as the origins of life were pushed back, natural selection became a more reasonable mechanism of evolution (Darwin 1866: 371).

Defending Eozoön 

Dawson very early defended the biological nature of Eozoön (Dawson 1865b), continued until the end of his life (Dawson 1901), and was never convinced by any of the conflicting evidence presented by his critics. He even published two books on Life’s Dawn on Earth (Dawson 1876, 1897), in which he claimed Eozoön to be the starting point of creation. Indeed, Dawson was an ardent anti-Darwinist and did not believe in the quickly spreading theory of evolution. Thus, he was not amused at all that Darwinists jumped on his discovery and embraced it as support for their theory. He wrote (Dawson 1876: 227):

There is no link whatever in geological fact to connect Eozoön with the Mollusks, Radiates, or Crustaceans of the succeeding [rock record] … these stand before us as distinct creations. [A] gap … yawns in our imperfect geological record. Of actual facts [with which to fill this gap], therefore, we have none; and those evolutionists who have regarded the dawn-animal as an evidence in their favour, have been obliged to have recourse to supposition and assumption

In other words, Dawson thought that the “discovery of his ‘dawn animal’ had exposed the greatest missing link in the entire fossil record, a gap so enormous that it served to unmask the myth of evolution’s claimed continuity” (Schopf 2000, Wilson 2011). What an irony, which also shows how very differently the same fossil evidence can be interpreted by distinguished scientists.

In modern paleontology it is still a very common phenomenon that fossils are over-interpreted by the scientists and over-hyped in the media as undeniable and unequivocal proof for Darwinian evolution. Whenever you come across press releases that boldly claim a new fossil rewrites the history of life, represents a long-sought transitional form or missing link, or proves the gradual evolution of certain organs and body plans, all alarm bells should ring. This is usually a clear sign that the scientists have gone far beyond an objective description of the empirical evidence and are driven by the desire to support evolutionist hypotheses. Apparently, since the time of Darwin and Dawson, some things have not changed much.

References

Adelman J 2007. Eozoön: debunking the dawn animal. Endeavor 31(3), 94–98. DOI: https://doi.org/10.1016/j.endeavour.2007.07.002

Carter HF 1874a. On the structure called Eozoon canadense in the Laurentian limestone of Canada. Annals and Magazine of Natural History (Ser. 4) 13(75), 189–193. DOI: https://doi.org/10.1080/00222937408680843

Carter HF 1874b. On the structure called Eozoon canadense in the Laurentian limestone of Canada. Annals and Magazine of Natural History (Ser. 4) 13(77), 376–378. DOI: https://doi.org/10.1080/00222937408680882

Carter HF 1874c. Eozoon canadense not a foraminifer or calcareous rhizopod secretion. American Journal of Science and Arts (Ser. 3) 7, 437–438. 

Dana JD 1865. On the History of Eozoön Canadense. American Journal of Science s2-40(120), 344–362. DOI: https://doi.org/10.2475/ajs.s2-40.120.344

Darwin CR 1866. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London (UK), p. 371. http://darwin-online.org.uk/content/frameset?pageseq=1&itemID=F385&viewtype=text

Dawson JW 1865. On the Structure of Certain Organic Remains in the Laurentian Limestones of Canada. Quarterly Journal of the Geological Society 21(1–2), 51–59. DOI: https://doi.org/10.1144/GSL.JGS.1865.021.01-02.12

Dawson JW 1876. Life’s Dawn on Earth Being the History of the Oldest Known Fossil Remains and Their relations to geological time and the development of the Animal Kingdom. Hodder & Stoughton, London (UK), 239 pp.

Dawson JW 1897. Relics of Primeval Life: Beginning of Life in the Dawn of Geological Age. Fleming H. Revell Company, New York (NY), 336 pp. 

Dawson JW 1901. Fifty years of Work in Canada Being Autobiographical Notes by Sir William Dawson, C.M.G., LL.D., F.R.S. Etc. Etc. Ballantyne, Hanson, & Co., London (UK), 308 pp.

Dawson JW & Carpenter WB 1865. Notes on Fossils recently obtained from the Laurentian Rocks of Canada, and on objections to the organic nature of Eozoon. 367–366. Quarterly Journal of the Geological Society 23, 257–265. DOI: https://doi.org/10.1144/GSL.JGS.1867.023.01-02.40 

Dolan JR 2023. The saga of the false fossil foram Eozoon. European Journal of Protistology 87(2):125955, 38 pp. DOI: https://doi.org/10.1016/j.ejop.2022.125955

Hahn O 1876. Is there such a thing as Eozoon canadense? A microgeological investigation. The Annals and Magazine of Natural History 17(100), 265–282. https://archive.org/details/biostor-92657 (English translation of German article: Hahn O 1876. Giebt es ein Eozoon canadense? Eine mikrogeologische Untersuchung von Otto Hahn in Reutlingen. Jahreshefte des Vereins für vaterländische Naturkunde in Württemberg 32, 132–155. http://darwin-online.org.uk/content/frameset?pageseq=1&itemID=A487&viewtype=text)

Johnston-Lavis HJ & Gregory JW 1894. Eozoonal structure of the ejected blocks of Monte Somma. The Scientific Transactions of the Royal Dublin Society (Ser. 2) 5, 259–286.

Logan WE 1864. On organic remains in the Laurentian Rocks of Canada. American Journal of Science and Arts 37, 272–273.

Logan WE 1865. On the Occurrence of Organic Remains in the Laurentian Rocks of Canada. Quarterly Journal of the Geological Society 21, 45–50. DOI: https://doi.org/10.1144/GSL.JGS.1865.021.01-02.11

Lyell C 1864. Extracts from the Address of the President Sir Charles Lyell, D.C.L., F.R.S. Canadian Naturalist and Geologist 1, 389–403.

Meyer SC 2013. Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. HarperOne, New York (NY), viii+498 pp. https://darwinsdoubt.com

Möbius K 1878. Der Bau des Eozoon canadense nach eigenen Unterschungen verglichen mit dem Bau der Foraminifera. Paleontographica 25(5-6), 175–194. https://www.schweizerbart.de/papers/palae/detail/25/59572/Der_Bau_des_Eozoon_c

Moon TJ, Mann PB & Otto JH 1947. Modern Biology. Henry Holt and Company, New York (NY), 664 pp. 

O’Brien CF 1970. Eozoön Canadense: “The Dawn Animal of Canada”. Isis 61(2), 206–223. DOI: https://doi.org/10.1086/350620

O’Connor A 2023. Canadian Pseudo-fossil: This specimen was once thought to represent the earliest life on Earth. National Museum of Ireland website. https://www.museum.ie/en-IE/Collections-Research/Collection/Documentation-Discoveries/Artefact/A-Canadian-Pseudo-fossil/4272e35f-065a-4605-9be0-90a3404eada2

Schopf JW 2000. Solution to Darwin’s dilemma: Discovery of the missing Precambrian record of life. PNAS 97(13), 6947–6953. DOI: https://doi.org/10.1073/pnas.97.13.6947

Wilson M 2011. Wooster’s “Fossil” of the Week: The most famous pseudofossil ever (Proterozoic of Canada). Wooster Geologists May 8, 2011. https://woostergeologists.scotblogs.wooster.edu/2011/05/08/wooster’s-fossil-of-the-week-the-most-famous-pseudofossil-ever-proterozoic-of-canada/

Designed to connect?

 

Yet more colliding titans.

 

Things to consider before buying that slightly used theory from OOL science's pitchmen?

 

The post truth world on steroids?

 

The father of the bomb?

 

On the science of fireworks.

 

The fundamental constant is not constant?

 

..Just enough religion to make us hate.." continued.

 

James Tour on origin of life science etc.

 

More light ,less heat on OOL science's conundrums

 

Yet more on academia's replication crisis.

 

On Trinitarians' public enemy no.1

 

Oliver Cromwell: a brief history.

 

Go to the ant and be instructed?

 Ants Build Landmarks for Navigation

David Coppedge

Picture being alone on a featureless planet. You’ve just left your underground station and are seeking minerals necessary to supply the base. Soon, the station entrance vanishes from sight as you continue searching. When you find the minerals, you turn around and have forgotten the way home! The horizon all around you is a monotonous waste. You wish you had left breadcrumbs like Hansel and Gretel, or better yet, had built a tall visible tower where the base is. 

This is the plight faced by Cataglyphis fortis ants that live on a salt pan in Tunisia. Tree ants and rock ants do not have this problem; they have plenty of landmarks. But the ones that live on the salt pan are surrounded by a white, flat horizon in all directions. Along the shoreline there are visual cues, but those out in the middle of the playa have few to none. The ants face death from heat exhaustion as they forage under the hot sun alone, walking fast to keep their feet from overheating. Scientists from Germany were intrigued how they can almost always navigate their way back to the nest. 

Eric Cassell discussed ant navigation in Animal Algorithms, noting that with brains only a quarter the size of a honeybee brain, ants “produce exquisitely efficient, robust navigation in complex environments” with their 250,000 neurons. As mentioned for the salt pan, simple environments without landmarks can be no less challenging. The situation calls for exceptional methods of path integration, especially for solitary foragers like C. fortis. For path integration to work, the ants need a neural compass and neural odometer and memory to store the global vector, Cassell says. The global vector can also be informed by odor trails, a polarized light compass and sun compass, and by landmarks.

Landmark Foresight

The successful strategy of C. fortis ants was revisited recently in Current Biology by Freire, Bollig, and Knaden. Their observations and experiments showed that the ants build landmarks on the journey out — but only when needed. Commenting on the research in the same issue, Cornelia Buehlmann rhapsodized about the architectural abilities of ants and many other creatures.

When we look at structures built by animals, we instantly appreciate that animals are naturally better architects than most humans. For example, beavers build fascinating constructions containing dams and dome-shaped lodges; birds construct elaborated nests; badgers form setts consisting of extensive underground networks of tunnels and chambers; termites build enormous mounds that can be a few metres in height; and ants build amazingly complex nest structures in many sizes and shapes. The key purpose of most homes is to provide a safe shelter for its inhabitants. Animals need to be safe from harsh weather conditions, hide from prey or house their offspring. Most animals have optimised the way of building their homes to get the best possible protection. Termites and ants, for example, have the ability to build nest mounds that allow perfect thermoregulation and ventilation and also protect from occasional flooding. Of course, nest structures can also have other functions: bird nests, for example, can play a role in sexual selection. A new study reported in this issue of Current Biology by Freire et al. now shows that nest hills from desert ant colonies not only provide a safe home but that they are built as visual landmarks and are crucial for successful navigation.

The height of the nest hill is one strategy used by C. fortis ants for navigation. The entrance hill can be up to 10 cm high, visible tens of meters away. Some foraging ants, though, travel up to 1 km away, beyond line-of-sight visibility. This new measurement, longer than previously recorded for this species, shows that ants must be able to use multiple cues for path integration.

Experimental Setup

To see if the ants use their tall nest hills for navigation, the research team removed 16 nest hills at sites deep in the salt pan too far out for visual cues from the shoreline. They placed cookie crumbs at various distances to tempt foragers to venture out. Adjacent to half of the nest entrances, they placed 50-cm black cylinders as artificial landmarks, then followed individual foraging ants at a safe distance. They found that the ants were able to use the artificial landmarks to get back, but navigation was impaired without the cylinders. At those sites, they observed the ants inside the colony busily rebuilding their nest hills. This proved that the height of the nest hill is important as a visual landmark, not just for flood protection or thermoregulation. Buehlmann comments,

These results show that ants are less likely to build these hills when other landmarks are available. This is a fascinating finding that suggests that ants sensibly decide whether it is necessary to build a nest hillthat facilitates the accurate localisation of the nest entrance.

To Buehlmann, this implies that “Small-brained animals have the cognitive ability to control the colonies’ navigational success.” As a result, fewer individuals die of heat exhaustion or are killed by a predator.

Foraging in the salt pan is a race against time. About 20 percent of the foraging ants that were displaced by the researchers died in the desert sun while trying to find their way back. Other arthropods routinely die in the heat, too, providing a main source of food for the C. fortis ants. The cookie crumbs were undoubtedly a treat. One ant got as far as 2 km out but didn’t make it back. The record for distance and successful return with its cookie crumb was 1.1 km — probably near the limit of its physical ability. So far from its visual cue, it must have relied on other cues to successfully integrate its path back home. 

Investment Wisdom and Information Flow

The importance of having a tall nest was a surprise to the research team:

We were surprised that Cataglyphis ants not only build their own nest-associated landmarks but also do so readily when deprived of other visual cues necessary for navigation. A colony’s investment into building a nest hill is justified when other guiding visual cues are absent, as fast and efficient homing is evidently paramount for survival in the harsh habitat of the salt pan. However, as soon as other visual cues are present, the investment does not seem justified anymore and no nest hill is rebuilt. 

The whole colony must be involved in the investment of having a tall landmark.

Foraging is usually the last task in the life of a Cataglyphis worker, while the digging involved in building the nest hill is often performed by younger ants. This calls for some kind of information flow between the older foraging ants that face the lack of visual cues surrounding the nest and their younger nestmates responsible for building the nest-defining landmark.

How Do They Know?

If the younger ants do the work of rebuilding the nest hill, Buehlmann wonders how they know to get to work on the project.

If so, how do they know whether there is a lack of nest-defining cues around the nest? At the start of an ant’s foraging career, ants do well-choreographed learning walks around the nest. Their general purpose is the acquisition of information about the visual surrounds of the nest with relation to celestial compass cues. Future experiments will need to reveal the mechanisms of the described nest building behaviour and show who is triggering the hill re-building. It will be exciting to learn how individual foraging and navigation relates to colony-level nest building activities and if and how information is shared between nestmates about the need to build a nest hill for navigational purposes.

Beyond Machinery

In this extreme case of life-or-death navigaton, the ants show themselves remarkably well equipped. They are born into the world with sensors, algorithms, and integrated systems of moving parts supplied by nutrients and machines that enable them to walk fast under the hot sun and perform sophisticated navigation. But more is required.

Of interest in the context of the design debate, information flow is once again shown to be central to the story. Having neurons packed into a tiny brain is important, but neurons are useless without information. Information is an intangible, nonphysical, conceptual reality that makes life work. Information is the substrate on which life operates, and wisdom is the effective use of information. It can be programmed into code, but wisdom is the bequest of a beneficent and capable mind.

On the metaphysics of science?

 Can Science Escape Faith-Based Beliefs? Maybe It Needs Them!

Denyse O Leary

Physicist and astronomer Marcelo Glieser offered some thoughts recently on faith and science, noting that the scientific revolution has hardly changed the picture of faith much: “the great scientific advances of the past four centuries have not radically diminished the number of believers” in transcendent realities

If science is to help us, in the words of the late Carl Sagan, by providing a “candle in the dark,” it will have to be seen in a new light. The first step in this direction is to admit that science has fundamental limitations as a way of knowing, and that it is not the only method of approaching the unattainable truth about reality. Science should be seen as the practice of fallible humans, not demigods. We should confess our confusion and acknowledge our sense of being lost as we confront a Universe that seems to grow more mysterious the more we study it. We should be humble in our claims, knowing how often we must correct them. We should, of course, share the joy of discovery, the achievements of human inventiveness, and the importance of doubt. 

MARCELO GLEISER, “FAITH-BASED BELIEFS ARE INESCAPABLE IN SCIENCE,” BIG THINK, JUNE 28, 2023

As he implies, there’s no reason why it should. Science, for better or worse, is a faith-based enterprise. Along with many easier quests, scientists continue to pursue outliers like the origin of life, whether there is life in remote star systems, and the nature of consciousness. Many such topics border on metaphysics and may well involve imponderables. But then finding the right answer might not be as important in some cases as developing the right questions.

Why must scientists have faith that we can make progress in understanding our world? Political analyst M. Anthony Mills proposes at least three general ideas about what science does. What we expect science to do for us largely depends on which one of them we adhere to.

First Model

The first is what we might call the accumulationist model of scientific progress. According to this model, science progresses through the steady accumulation of data, facts, or information. The guiding metaphor here is the container: scientists go out and find bits of knowledge and add them to the container. Scientific progress is therefore a cumulative process, linear and gradual.

M. ANTHONY MILLS, “WHAT DOES ‘SCIENTIFIC PROGRESS’ MEAN, ANYWAY?” THE NEW ATLANTIS, SPRING 2023 

This model is popular but it can lead us astray. “Science will find the answer!” is only meaningful if the question is framed in a way that science can address. Science can’t tell us whether we are our brother’s keeper, whether it profits us to gain the whole world if we lose our souls, or whether some unfortunate person’s life is worth living. Unfortunately, science is sometimes misused to add apparent weight to a given answer, when the question is really one of ultimate spiritual values, not of science.

Second Model

Another model is what Mills calls “Kuhnian,” after the famous philosopher of science Thomas Kuhn (1922–1996), who introduced the concept of paradigm shifts in science:

According to this account, progress is not linear and gradual; it is punctuated by moments of profound conceptual change and innovation. There are periods of relative calm — what Kuhn termed “normal” science — during which progress looks a lot like it does to the accumulationist. But these periods are interrupted by crises, when prevailing theories break down. Rivals emerge, challenge the consensus, ultimately overthrow a prevailing paradigm, and take its place, as when relativistic and quantum physics dethroned classical physics. These are the scientific revolutions that Kuhn called “paradigm shifts.”  

M. ANTHONY MILLS, “WHAT DOES “SCIENTIFIC PROGRESS” MEAN, ANYWAY?” THE NEW ATLANTIS, SPRING 2023

When we are contemplating a vast historical sweep, Kuhn’s theories are indeed helpful. But on the ground, we usually can’t know for sure whether we are living in a massive paradigm shift. Theories rise and fall all the time. Which of the changes matter? For example, findings from the James Webb Space Telescope upended a variety of assumptions but how much they will change the basic paradigm remains to be seen.

Third Model

He calls the third model Baconian, after the early modern philosopher of science Francis Bacon (1561–1626):

According to the third model, however, science progresses not by extending existing scientific paradigms, nor by resolving problems or crises internal to science. Instead, science progresses by grappling with problems posed to it from outside by social, political, and economic needs. We recognize scientific progress not by advances or innovations in our theoretical knowledge but by whether and to what extent our theories help us solve practical problems. Does science generate technological breakthroughs, contribute to economic growth, or help us solve pressing social and political problems?  

M. ANTHONY MILLS, “WHAT DOES “SCIENTIFIC PROGRESS” MEAN, ANYWAY?” THE NEW ATLANTIS, SPRING 2023

Of course, if we rely entirely on the third model, we might reject science that isn’t telling us what we want to hear, even if what it is telling us is true and important.

Generally, as Mills acknowledges, we must try all three models to see how much each can contribute to our understanding. But each model requires an initial input of faith: Faith that a big picture will emerge from small contributions (Model 1), faith that we will recognize when theories must change (Model 2), and faith in a bigger picture of the universe that we don’t allow our current issues to completely obscure (Model 3).

No matter how scientists navigate between models, Gleiser thinks that, for creativity in science, faith is indispensable:

A scientist therefore must base their approach on an imponderable process that some call a hunch or an intuition. This is an intellectually guided expression of faith in how the scientist imagines the world to be. There is no way to venture into the unknown without this guiding light, and that light comes from a source that is not completely known. This is where science meets faith.

MARCELO GLEISER, “FAITH-BASED BELIEFS ARE INESCAPABLE IN SCIENCE,” BIG THINK, JUNE 28, 2023 

It’s hard to imagine creativity in science working any other way.

Finding context for the sophistication of primeval technology

 Something Is Missing from the Materialist Framework

Stephen J Iacoboni

In sketching here what I have called the science of purpose, I have argued that the best way to topple the materialist paradigm is to reverse the fundamental concepts of structure and function. (See, most recently, “Replacing Chemistry with Purpose.”) The framework of materialism is based on randomness, from which, combined with natural selection, any structure theoretically can arise. In this way of thinking, over billions of years, randomly generated structures accidentally began to perform functions, resulting in life on Earth as we know it. That is, all the seemingly designed function in the biosphere is simply a result of randomly generated structures. The appearance of design is an illusion.

What is not an illusion, not even to materialists, is the nearly unfathomable complexity of function carried out, nanosecond by nanosecond, in every living creature since life first arose. From the time you started reading this article, perhaps 60 seconds ago, trillions upon trillions of discrete exquisitely tuned chemical reactions took place in your body. And that has been going on since the time that your father’s sperm met your mother’s egg.

And so of course no one argues the fact that function is real. 

But Is It Designed?

The funny thing about function is that it is utterly dependent on context. You could have cells with insulin receptors so that glucose is allowed into the cytoplasm from the extracellular compartment. That chemical reaction, even by itself, is enormously complex. But then what? Without all the necessary enzymes to convert glucose and oxygen into ATP, which is another 20 or so extraordinarily exquisite metabolic steps, the entry of glucose into the cell by itself is meaningless. Purpose is only served when the entire series of molecular events achieves the end, the telos, that it was designed to accomplish: benefit the host.

This straightforward analysis creates a conundrum for the materialist who wants to maintain that function emerges out of randomly generated structures. Let’s say the primordial soup randomly generated lipid-encasing vesicles that let glucose in and out. You might call this a mechanical operation, but it is not a function. Function only has meaning when it serves a purpose, and purpose only materializes when it serves a self.

It Is Really That Simple

Function and purpose are meaningless terms absent a self that benefits from their realization. You can pound a board with a hammer all you want. But until you put a nail between the hammer and the board, so that the board attaches to some other object that creates a structure that achieves the end that the carpenter intended, you have accomplished nothing. No function has been carried out. No purpose served.

Professor Terrence Deacon, a distinguished biological anthropologist as well as a widely published author and materialist, has described this confusing state of affairs, even coining a word, “ententional,” to help to characterize it. In his book Incomplete Nature: How Mind Emerged from Matter, he asks how “teleological appearances of living processes [can] be accounted for…Investigators could neither accept ententional properties as foundational nor deny their reality, despite this apparent incompatibility.” (p. 147)

Scientists have learned over the centuries that when a fundamental theoretical impasse is encountered, we do not blame nature. We must blame the theory that fails to account for the observed natural phenomenon.

Something is missing from the theoretical framework of natural science if it cannot explain the function and purpose that are ubiquitous in life. And yes, the answer is there in plain sight in Professor Deacon’s own words. The truth is that “intentional” properties are foundational. They are the genesis of all purpose in life. 

The rise and fall of black excellence?

 

Finally, an electric truck?

 

Conditionalism is not a kook position?