Monday, 8 July 2024
On the irreducible complexity of asexual reproduction.
Herding Chromosomes in the Mitosis Corral
My head is swimming after reading several recent papers on cell division. The multiplicity of molecules involved, and how they get where they need to be and do what they need to do — it is all so astonishing, it beggars description. I wish there were better ways to communicate to laypersons the emotional impact of learning about cell biology without drowning them in jargon like this excerpt from one paper about centrosomes:
During interphase, Cep57 forms a complex with Cep63 and Cep152, serving as regulators for centrosome maturation. However, the molecular interplay of Cep57 with these essential scaffolding proteins remains unclear. Here, we demonstrate that Cep57 undergoes liquid–liquid phase separation (LLPS) driven by three critical domains (NTD, CTD, and polybasic LMN). In vitro Cep57 condensates catalyze microtubule nucleation via the LMN motif-mediated tubulin concentration. In cells, the LMN motif is required for centrosomal microtubule aster formation. Moreover, Cep63 restricts Cep57 assembly, expansion, and microtubule polymerization activity….
Specialists are comfortable with this kind of talk, but we have a world of students being told that cells “emerged” by chance, and “evolved” into humans by blind, purposeless processes over millions of years. The facts above scream “No way!” but how do we tell non-scientists that without burying them in unfamiliar terms? Analogies and pictures can only go so far. I try my best, but simple explanations cannot do justice to the reality.
For students whose knowledge of mitosis may be limited to light-microscope images of dividing cells, or high-school biology diagrams of the five stages of cell division (interphase, prophase, metaphase, anaphase, telophase —“Ho-hum, will that be on the test?”), let me try to unpack some of the awesome wonders hidden in the above paragraph. It comes from a paper in PNAS by 15 specialists at the Institute of Bioinformatics and Structural Biology in Taiwan’s National Tsing Hua University. Respond with applause at each line:
Some molecules join forces to control other molecules!
Molecules assemble in compartments without a membrane to work in harmony!
Important things won’t happen unless all the parts are together! — and bad things happen if they fail!
Biochemistry is not your normal chemistry, where molecules collide like bumper cars and sometimes join up or break up. This is robotic factory work at a high level. With apologies to Jonathan Maclatchie, who knows the jargon and wrote at a more scholarly level recently (here), and to all the other practicing scientists who talk like this as their daily routine, we have to get the hay down where the cows can eat it. Students become so indoctrinated into materialistic scientism by the time they reach grad school (if they seek a career at that level), it becomes difficult for them to buck the evolutionary consensus once they start learning the real guts of cell biology. One almost must achieve tenure before being able to see without evolutionary blinders on. It happened one day to Michael Behe when he stared at an electron micrograph of a bacterial flagellum, and pondered: “That’s an outboard motor. That’s not a chance assemblage of parts.” His thought started a Revolution.
With hopes of generating some of the awe I felt in my reading, here goes my translation of what this paper revealed. The PhDs can skip the lay talk by clicking the link to the research.
The Mitosis Ranch
Trying to visualize this, I thought of the following analogy. Say a rancher must duplicate the cows in a corral and create two corrals with identical numbers and types of cows. He first has his cowboys yoke identical cows together (yokes representing the centromeres). They line the cows up between the two corrals, head to tail. Then other cowboys rope the cows from opposite directions, lassoing specialized “horns” on the yokes — the kinetochores. It takes a few tries for a cowboy to lasso the horn on his side of the yoke, but each one keeps trying till succeeding. An inspector checks that each yoked pair has one and only one rope on each side, and that the ropes are taut. When he gives a signal (the checkpoint), another cowboy goes down the line and breaks the yokes. The cowboys then pull their cows into the opposite corrals, and a gate closes between them.
The reality in cell division is much, much more intricate, but something like that really happens every time a eukaryotic cell divides. Hundreds of “cowboys” know their roles and know when to go into action. In the cell, though, the “cowboys” are blind and work in the dark. Are we beginning to be astonished yet? There’s much more!
Temporary Meeting Spaces
The PNAS paper reveals new knowledge about how the right molecules come together in the centrosome, a structure critical for pulling chromosomes apart during cell division. In mitosis, there are two centrosomes, one on each side of the cell. Centrosomes are where the mitotic spindle sends out the “ropes” to pull the chromosomes apart into the daughter corrals. Within each centrosome, two marvelously-symmetric centrioles grow perpendicular to each other (see here). They will be the organizing centers for the spindle microtubules. Microtubules will grow out from the centrosome and attach to the chromosomes — one microtubule per sister chromatid — at specialized link points called kinetochores. Like a rope, each microtubule is composed of multiple strands of tubulin, conferring stability to each spindle fiber.
Incidentally, how do these distant centrosomes know how many chromosomes there will be and come up with the right number of microtubules? I asked an AI engine that question. It said,
The centrosome doesn’t inherently “know” the number of chromosomes. Instead, the process of microtubule formation is guided by checkpoints in the cell cycle and regulatory proteins. During mitosis, each pair of chromosomes attaches to a kinetochore, which then attaches to the spindle fibers formed from the centrosome. The number of chromosomes determines the number of kinetochores, which in turn helps regulate the number of microtubules needed for proper chromosome separation. It’s a complex and coordinated process involving many proteins and regulatory mechanisms
OK, Well; Point Taken
Back to the “temporary meeting spaces” at centrosomes. The centrosome has no membrane. But when Cep57 (centrosome protein #57 out of dozens known so far) is present, a temporary barrier forms around the required ingredients. This happens by “liquid-lipid phase separation” (LLPS), something like how oil droplets form in water (see my previous article on condensates here). But first, the temporary meeting space (peri-centriolar matrix, or PCM) has to grow by an order of magnitude, from 300 nanometers to micrometers, as all the required ingredients assemble. “Human Cep57,” they say, “is a coiled-coil scaffold at the pericentriolar matrix (PCM), controlling centriole duplication and centrosome maturation for faithful cell division.”
Before the onset of mitosis, the centriole undergoes centriole-to-centrosome conversion by recruiting more centrosomal components and expanding the PCM into a micron-sized structure. This expansion leads to an increase in the microtubule nucleation factors, facilitating the rapid assembly of the mitotic spindle during mitosis. It is a central question of how the PCM assembles into a dense compartment enriched with hundreds of different proteins in the human centrosome during PCM expansion. Liquid–liquid phase separation (LLPS) is a compelling concept for elucidating the organizational principles underlying membrane-less organelles. In LLPS systems, multivalent interactions through folded domains or intrinsically disordered regions drive phase separation, resulting in the formation of dynamic biomolecular condensates accessible to cognate clients
“Hundreds of different proteins.” Did you catch that? How do the right ones all end up within the membraneless condensate? How could blind evolution ever accomplish such a meet-up? Interestingly, the “intrinsically disordered regions” of some of these proteins, which might have been considered poorly designed by some, play a key role in the phase separation. Notice, too, that the condensate is “dynamic” and “accessible” to the “cognate clients” that belong there, while keeping non-members out.
The authors point out that a deficiency of just this one component, Cep57, results in disorganization of the PCM, and a terrible disease:
Cep57 mutations are genetically linked to mosaic-variegated aneuploidy (MVA), a rare disease characterized by an abnormal number of chromosomes. The MVA syndrome manifests in various disorders, including skeletal anomalies, microcephaly, and childhood cancers
Cep57 is not the only vital part. “Cep57, Cep63, Cep152, Cep192, CDK5RAP2 (Cep215), and pericentrin are essential scaffolding proteins for PCM integrity.”
How’s Your Awe Meter So Far?
It’s difficult to convey the wonder of these realities without getting bogged down in jargon and detail. For more awe, add these considerations:
All this takes place in spaces too tiny to see with the naked eye.
Scientists have only discovered most of these intricate details within the lifetimes of many alive today.
The sequence of amino acids in each protein involved is far too improbable to have originated by chance.
Several million cells divide every second in our bodies.
Cells have been dividing since the beginning of life on earth.
The accuracy of cell division is so extraordinarily high, many animals alive today are recognizable from their counterparts in the fossil record.
We are truly privileged to behold details of wonders that were concealed from the eyes of people for thousands of years. If Romans and Babylonians and ancient Chinese were impressed by the sight of a baby at birth, how much more should we be awestruck, dumbfounded, indeed reverent at what biochemists are learning today about realities too small for human eyes? Sure, some observations like evil and suffering are hard to understand, yet even these are better situated for explanation in a design context. As my college biology prof used to say, “The amazing thing is not that we get sick. The amazing thing is that we are ever well,” considering how many things must work correctly each moment of every day. Never become complacent about these realities taking place inside us. We are witnessing intelligent design at a level never comprehended throughout all human history.
Sunday, 7 July 2024
Engineerless engineering ? :Cosmic edition.
From Galaxies to Atoms, a Vast Web of Fitness for Life
On a classic episode of ID the Future, host Eric Anderson begins a conversation with biochemist Michael Denton about Denton’s 2020 book The Miracle of the Cell, part of his continuing Privileged Species series exploring nature’s fine tuning for life. New research keeps unveiling ever more ways in which this fine tuning exists, from the cosmos to the atoms of the periodic table, and even to the subatomic level of quantum tunneling. Says Denton: “The miracle of the cell completes the overall fitness paradigm that unites galaxies with atoms in a vast web of fitness for life.”
Denton helped launch the modern intelligent design movement with his seminal 1985 book Evolution: A Theory in Crisis. The book inspired a number of well-known ID scholars, including Michael Behe, Stephen Meyer, and William Dembski, to speak out on the limits of Darwinian processes and the evidence for intelligent design. Denton followed up in 1998 with Nature’s Destiny, a step-by-step argument for human inevitability and human uniqueness in the universe.
This is Part 1 of a two-part conversation. Find and listen to the podcast here. Look for Part 2 next!
Saturday, 6 July 2024
Friday, 5 July 2024
Another Friday,another nightmare for Darwinists, courtesy the fossil record.
Fossil Friday: Time Wanderers Debunk Popular Scenario of Mammalian Evolution
This Fossil Friday features the holotype of the shrew-sized fossil vertebrate Chronoperates paradoxus from the Early Tertiary (Late Paleocene) Paskapoo Formation of Alberta in Canada. I still remember very vividly, when I was a graduate student at the University of Tübingen the sensational discovery of this fossil hit the news in 1992 (Hecht 1992, Novacek 1992), which we discussed in the vertebrate phylogeny course of the late great Dr. Gerhard Mickoleit. What was so special about this find?
In their original description of the tiny fossil jaw fragment, Fox et al. (1992a) documented several unique features of the lower jaw and its dentition that are exclusively characteristic of primitive mammal-like reptiles of the order Therapsida and the suborder Cynodontia (both taxa were later redefined in cladistic classification to include true mammals). Therapsids first appeared in the Early Permian 280 million years ago and were believed to have become extinct in the Middle Jurassic about 160 million years ago. Therefore, this Paleocene fossil would have been 100 million years younger than the previous youngest fossil record of therapsids and double their stratigraphic range, implying a long ghost lineage. This is why the relict genus was named Chronoperates, which means time wanderer in Greek.
Immediately Contested
The determination of Chronoperates as a therapsid was immediately contested by vertebrate paleontologist Hans-Dieter Sues (2006), but defended by the original authors (Fox et al. 1992b), who emphasized that Sues had not presented any synapomorphies in support of his alternative mammalian determination, and also had never studied the actual specimen. Indeed, the main argument by Sues was a very vague appeal to the only subtle differences between the teeth of Chronoperates and those of Cretaceous symmetrodont mammals (also see Novacek 1992), which was a possibility that was actually already addressed and refuted in the original description, as well as the false and misleading claim that the therapsid features could rather be artefacts of preservation. Nevertheless, some other scientists also doubted a therapsid affinity but explicitly admitted that they “don’t have any alternative to offer” (Hopson quoted in Hecht 1992). McKenna & Bell (1997: 43) likewise did not believe in the non-mammalian cynodont identity, but rather suggested a “dubious” position, possibly among basal holotherians, which are Triassic and Jurassic stem mammals (see Naish 2006b). Naish (2006b) also mentioned that “Meng et al. (2003) noted that the medial dentary scar seen in Chronoperates might not house post-dentary bones, as Fox et al. proposed, but instead a persisting Meckel’s cartilage. Now, if Chronoperates did possess a Meckel’s cartilage, this would be a first for a post-Mesozoic synapsid, and would further support ideas that Chronoperates is actually a late-surviving basal mammal” as suggested by McKenna & Bell.
Until today the therapsid affinity of Chronoperates is generally considered to be debunked, and Chronoperates is listed as potential symmetrodont mammal in Wikipedia, all based on a single one-page article with some unsubstantiated sweeping comments by a scientist, who never studied the actual fossil himself. Nobody ever bothered to look at this sensational fossil again. The only reason why the skeptical view still prevailed, is that the fossil would be very much out-of-place and contradicting the expectations from the mainstream Darwinian scenario of mammal origins. So much about unbiased scientific quest for truth. If some facts don’t fit the narrative, just deny them and sweep them under the rug.
Other Out-of-Place Fossils
In his two-part blog post, vertebrate paleontologist Darren Naish (2006a, 2006b) also discussed some other out-of-place fossils of mammal-like reptiles (non-mammalia therapsids):
In 1915 several fragmentary fossil bones were discovered in Early Cretaceous sediments from Queensland in Australia, which exhibited remarkable similarities with the extinct Dicynodontia, a clade of Permian and Triassic herbivore non-mammalian therapsids that lacked any fossil record beyond the Triassic-Jurassic boundary. The surprising dicynodont affinity was later indeed strongly confirmed by Thulborn & Turner (2003), who meticulously demonstrated that neither the dating nor the phylogenetic position can be reasonably disputed. This is a big deal, because this fossil record of dicynodonts is again “something like 100 million years younger than the previously known youngest members of the group” (Naish 2006a). This arguably proves that a similar ghost lineage for Chronoperates would be well within the realm of possibility and no reason to reject its determination as therapsid. So, it is hardly surprising that just a few years later, Agnolin et al. (2010) claimed that the Australian bones may rather have belonged to an extinct group of crocodyliforms called Baurusuchia, just because of unspecified striking similarities without any further explanation or documentation, while Knutsen & Oerlemans (2020) disputed the dating (instead suggesting a Plio-Pleistocene age) and the determination all-together, but this time the bones were claimed to belong to a diprotodontid marsupial and suddenly found “no features diagnostic of dicynodonts.” Thulborn & Turner (2003) on the other hand had unequivocally stated that this fossil “clearly does not represent … any of the big marsupials such as Diprotodon … The only identification supported by positive evidence, in the form of demonstrable similarities and diagnostic features, is ‘dicynodont.’” As happens all too often, apparently everything goes by the board when the goal is to make inconvenient fossils fit the preferred story. It is sobering to realize how dubious and sloppy evolutionary biology actually works when you look a bit closer behind the pompous facade of the so-called “undeniable scientific facts.”
Simpson (1928) described the docodont Peraiocynodon inexpectatus from the Early Cretaceous Purbeck Limestone of England, which was confirmed as a docodont by Averianov (2004). The species name inexpectatus of course alludes to the unexpected young age of this fossil, because Docodonta are Mesozoic mammaliaforms that abruptly appeared in the fossil record of the Middle Jurassic and were believed to have gone extinct in the Late Jurassic. Maschenko et al. (2002) described with Sibirotherium another late surviving docodont from the Early Cretaceous of West Siberia, later complemented by another genus Khorotherium from the Early Cretaceous of Yakutia as the youngest known docodont (Averianov et al. 2018). The previously described assumed docodont Reigitherium from the Late Cretaceous of Patagonia (Pascual et al. 2000), was later recognized as a real mammal of the dryolestoid order Meridiolestida (Rougier et al. 2003, 2011, Harper et al. 2018), which may well be correct.
Finally, there is the unnamed Saint Bathans mammal from the Early Miocene (18.7-15.9 mya) of New Zealand (Worthy et al. 2006), which is known from three fragmentary specimens and seems to represent a basal mammaliaform outside the crown group clade of monotremes, marsupial and placental mammals, and even basal of the extinct multituberculate branch. It is technically not a non-mammalian therapsid but also not a crown group mammal. Therefore, the discovery of such a primitive stem mammal in Miocene layers was highly unexpected and surprising (Naish 2006b).
Survivors or Relics
All these late survivors or relicts (sometimes called Lazarus taxa) are not just some weird scientific curiosities, but actually demonstrate a general problem with the common evolutionary narrative about mammalian origins, which claims that mammal-like reptiles disappeared because they were outcompeted by the modern true mammals. Mammal-like reptiles like pelycosaurs and therapsids ruled the Permian and Triassic periods, and some therapsids like the herbivorous Tritylodontidae existed till the Jurassic. All these alleged early ancestors of mammals were thought to have been wiped out by the more modern real mammals (Mammaliaformes), which originated in the Triassic but did not diversify before the Late Jurassic. This widely accepted replacement theory was overturned for good, when more than 250 tritylodontid teeth were discovered in Early Cretaceous layers of Japan (Matsuoka et al. 2016), proving that tritylodontids survived 30 million years longer than previously believed. Tritylodontids demonstrably coexisted for millions of years with more modern mammaliaforms that partly even occupied the same herbivorous niches. The crude Darwinist presumption of more advanced descendants outcompeting their primitive ancestors turned out to be wrong once again. The take-home message is this: Darwinian stories are exactly that — just fancy stories rooted in wishful thinking rather than in hard science.
References
Agnolin FL, Ezcurra MD, Pais DF & Salisbury SW 2010. A reappraisal of the Cretaceous non-avian dinosaur faunas from Australia and New Zealand: Evidence for their Gondwanan affinities. Journal of Systematic Palaeontology 8(2), 257–300. DOI: https://doi.org/10.1080/14772011003594870
Averianov AO 2004. Interpretation of the Early Cretaceous mammal Peraiocynodon (Docodonta) and taxonomy of some British Mesozoic docodonts. Russian Journal of Theriology 3(1), 1–4. https://zmmu.msu.ru/rjt/articles/ther3_1_01_04_Averianov.pdf
Averianov A, Martin T, Lopatin A, Skutschas P, Schellhorn R, Kolosov P & Vitenko D 2018. A high-latitude fauna of mid-Mesozoic mammals from Yakutia, Russia. PLoS ONE 13(7):e0199983, 1–17. DOI: https://doi.org/10.1371/journal.pone.0199983
Fox RC, Youzwyshyn GP & Krause DW 1992a. Post-Jurassic mammal-like reptile from the Palaeocene. Nature 358(6383), 233–235. DOI: https://doi.org/10.1038/358233a0
Fox RC, Youzwyshyn GP & Krause DW 1992b. Palaeocene therapsid debate. Nature 360, 540. DOI: https://doi.org/10.1038/360540a0
Harper T, Parras A & Rougier GW 2018. Reigitherium (Meridiolestida, Mesungulatoidea) an Enigmatic Late Cretaceous Mammal from Patagonia, Argentina: Morphology, Affinities, and Dental Evolution. Journal of Mammalian Evolution 26(4), 447–478. DOI: https://doi.org/10.1007/s10914-018-9437-x
Hecht J 1992. Science: Riddle of the ‘time wanderer’. NewScientist August 29, 1992. https://www.newscientist.com/article/mg13518363-300-science-riddle-of-the-time-wanderer/
Knutsen EM & Oerlemans E 2020. The last dicynodont? Re-assessing the taxonomic and temporal relationships of a contentious Australian fossil. Gondwana Research 77, 184–203. DOI: https://doi.org/10.1016/j.gr.2019.07.011
Maschenko EN, Lopatin AV & Voronkevich AV 2002. A new genus of tegotheriid docodonts (Docodonta, Tegotheriidae) from the Early Cretaceous of West Siberia. Russian Journal of Theriology 1(2), 75–81. DOI: https://doi.org/10.15298/rusjtheriol.01.2.01
Matsuoka H, Kusuhashi N & Corfe IJ 2016. A new Early Cretaceous tritylodontid (Synapsida, Cynodontia, Mammaliamorpha) from the Kuwajima Formation (Tetori Group) of central Japan. Journal of Vertebrate Paleontology 36(4): e1112289, 1–16. DOI: https://doi.org/10.1080/02724634.2016.1112289
McKenna MC & Bell SK 1997. Classification of Mammals Above the Species Level. Colombia University Press, New York (NY), xii+631 pp. https://books.google.at/books?id=zS7FZkzIw-cC
Meng J, Hu Y, Wang Y & Li C 2003. The ossified Meckel’s cartilage and internal groove in Mesozoic mammaliaforms: implications to origin of the definitive mammalian middle ear. Zoological Journal of the Linnean Society 138, 431–448. DOI: https://doi.org/10.1046/j.1096-3642.2003.00064.x
Naish D 2006a. ‘Dicynodonts that didn’t die: late-surviving non-mammalian synapsids I. Tetrapod Zoology May 23, 2006. http://darrennaish.blogspot.com/2006/05/dicynodonts-that-didnt-die-late.html
Naish D 2006b. ‘Time wandering’ cynodonts and docodonts that (allegedly) didn’t die: late-surviving synapsids II. Tetrapod Zoology May 25, 2006. http://darrennaish.blogspot.com/2006/05/time-wandering-cynodonts-and-docodonts.html
Novacek MJ 1992. Wandering across time. Nature 358(6383), 192. DOI: https://doi.org/10.1038/358192a0
Pascual R, Goin FJ, González P, Ardolino A & Puerta PF 2000. A highly derived docodont from the Patagonian Late Cretaceous: evolutionary implications for Gondwanan mammals. Geodiversitas 22(3), 395–414. https://sciencepress.mnhn.fr/en/periodiques/geodiversitas/22/3/un-docodonte-tres-derive-du-cretace-superieur-de-la-patagonie-implications-evolutives-pour-des-mammiferes-gondwaniens
Rougier G, Novacek MJ, Ortiz-Jaureguizar E, Pol D & Puerta P 2003. Reinterpretation of Reigitherium bunodontum as a Reigitheriidae dryolestoid and the interrelationships of the South American dryolestoids. Journal of Vertebrate Paleontology 23(Supp. 3), 90A. DOI: https://doi.org/10.1080/02724634.2003.10010538
Rougier GW, Apesteguía S & Gaetano LC 2011. Highly specialized mammalian skulls from the Late Cretaceous of South America. Nature 479 (7371), 98–102. DOI: https://doi.org/10.1038/nature10591
Simpson GG 1928. A Catalogue of the Mesozoic Mammalia in the Geological Department of the British Museum. British Museum (Natural History), London (UK), 215 pp.
Sues H-D 1992. No Palaeocene ‘mammal-like reptile’. Nature 359, 278. DOI: https://doi.org/10.1038/359278a0
Thulborn T & Turner S 2003. The last dicynodont: an Australian Cretaceous relict. Proceedings of the Royal Society of London B 270(1518), 985–993. DOI: https://doi.org/10.1098/rspb.2002.2296
Worthy TH, Tennyson AJD, Archer M, Musser AM, Hand SJ, Jones C, Douglas BJ, McNamara JA & Beck RMD 2006. Miocene mammal reveals a Mesozoic ghost lineage on insular New Zealand, southwest Pacific. PNAS 103(51), 19419–19423. DOI: https://doi.org/10.1073/pnas.0605684103
Thursday, 4 July 2024
The brain is more complex than the universe it contemplates?
Research: Our Brains Float Between Two Phases, Dodging Disorder
Anyone who has felt the need for several overflow brains just to keep up with a busy day will know the dread of a cartoon-like collapse. The good news, according to recent research, is that unsteadiness is the normal state of the human brain.
As science writer Carly Cassella puts it at ScienceAlert, “The human brain’s complexity verges on the brink of chaos, physicists say.” Our minds just never quite get used to it.
Poised Between Two Phases Without Collapsing
The physicists are Helen Ansell and István Kovács of the Physics and Astronomy Department at Weinberg College of Arts and Sciences at Northwestern University in Illinois. Examining the anatomy of neurons in the brains of humans, mice and fruit flies, they found that the cellular structure of the brain sits at a point that is poised between two phases:
When a magnet is heated up, it reaches a critical point where it loses magnetization. Called “criticality,” this point of high complexity is reached when a physical object is transitioning smoothly from one phase into the next…
Now, a new Northwestern University study has discovered that the brain’s structural features reside in the vicinity of a similar critical point — either at or close to a structural phase transition.
NORTHWESTERN UNIVERSITY. “BRAIN’S STRUCTURE HANGS IN ‘A DELICATE BALANCE,’” SCIENCEDAILY, 10 JUNE 2024. THE PAPER IS OPEN ACCESS.
The researchers don’t know whether this state is universal in brains as only three types have been studied so far.
Like Ice Becoming Water
No one has yet named the phases that the brains’ structures seem to hover between:
“The structure of the brain at the cellular level appears to be near a phase transition,” said Northwestern’s Helen Ansell, the paper’s first author. “An everyday example of this is when ice melts into water. It’s still water molecules, but they are undergoing a transition from solid to liquid. We certainly are not saying that the brain is near melting. In fact, we don’t have a way of knowing what two phases the brain could be transitioning between. Because if it were on either side of the critical point, it wouldn’t be a brain.”
NORTHWESTERN. ““A DELICATE BALANCE”
So how do the researchers know that these brains are near a phase transition?
Brain cells are arranged in a fractal-like statistical pattern at different scales. When zoomed in, the fractal shapes are “self-similar,” meaning that smaller parts of the sample resemble the whole sample. The sizes of various neuron segments observed also are diverse, which provides another clue. According to Kovács, self-similarity, long-range correlations and broad size distributions are all signatures of a critical state, where features are neither too organized nor too random. These observations lead to a set of critical exponents that characterize these structural features.
NORTHWESTERN. ““A DELICATE BALANCE”
Cassella offers
In the past, some scientists have suspected that phase transitions play an important role in biological systems. The membrane that surrounds cells is a good example. This lipid bilayer fluctuates between gel and liquid states to let proteins and liquid in and out.
By contrast, however, the central nervous system may teeter on a critical point of transition, while never actually becoming something else.
CARLY CASSELLA, SCIENCEALERT
Cassella’s comparison to the cell membrane is apt. Perhaps it will turn out that a slush environment is essential for a structure as complex as a brain. Forced into one phase only, it might start to malfunction.
The Human Brain Is a Lot Like the Universe
If we find these outcomes odd, it’s helpful to keep in mind that the human brain, for example, also has many similarities to the universe itself. Among others
Your brain is made up of a complex network of nearly 100 billion neurons that form 100 trillion neural connections. Neurons are clustered into a hierarchical network of nodes, filaments, and interconnected neural clusters that shape the complex thoughts, feelings, and emotions you experience. But these neurons make up less than 25 percent the mass of your brain, leaving the remaining 75 percent as water.
In a bizarre coincidence, the observable universe also contains an estimated 100 billion galaxies. The teetering balance between the pull of gravity and the accelerated expansion of the universe forms a cosmic web of string-like filaments composed of ordinary and dark matter.
TIM CHILDERS, “THE HUMAN BRAIN LOOKS SUSPICIOUSLY LIKE THE UNIVERSE, WHICH MAY FREAK YOU OUT,” POPULAR MECHANICS, NOVEMBER 17, 2020
Seen from that perspective, the brain’s delicate hover between two phases is just one of many remarkable facts about it.
And still even yet more on primeval tech's defiance of Darwinism.
Irreducible Complexity in Bacterial Cell Division
Ready to dip a toe in the ocean of biological ingenuity? Dr. Jonathan McLatchie is back, this time to discuss with me the engineering elegance and irreducible complexity of the process of bacterial cell division. You may wonder why we should care about something so miniscule as bacterial cells. After all, something so insignificant and unseen has little bearing on our daily lives. But if we’ve learned anything in the biological revolution of the 20th century, it’s that consequential things often come in very small packages. And if even the simplest forms of life exhibit stunning complexity and engineering prowess, all the more do we! And that complexity and design demands an adequate explanation.
Dr. McLatchie starts by reminding us what the term irreducible complexity means. It actually goes right back to a criterion of failure that Charles Darwin himself offered up regarding his theory of evolution: “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”
Then McLatchie describes the remarkable process of cell wall breakage and re-synthesis that allows cell division to take place. He explains why it’s a challenge for evolution: “Evolutionary processes cannot select for some future utility that is only realized after passing through a maladaptive intermediate,” says McLatchie. He also refutes the co-option argument, the claim that one part of the process might have been borrowed from one system and co-opted into another through evolution. Evolutionary processes don’t have the ability to look forward. For that, you need foresight, a power that our universal experience shows to be unique to intelligent agents. Find and listen to the podcast here.
Wednesday, 3 July 2024
File under "Well said" CVIII
" Never kiss a fool,
Never let a fool kiss you,
And Never let a kiss fool you."
Anonymous graffiti writer
On determining the canon re:"science"
What Is Pseudoscience? A Philosopher Tries to Figure It Out
Philosopher Massimo Pigliucci has carved part of his career out of efforts to identify pseudoscience and separate it from virtuous science. Two of his books are Nonsense on Stilts: How to Tell Science from Bunk (U Chicago Press 2018) and Philosophy of Pseudoscience (U Chicago Press 2013), co-edited with Maarten Boudry.
He thinks that any suggestion that our minds are not merely what our brains do is “antiscientific” and that there is no free will. So it’s worth noting that, in a recent article at Skeptical Inquirer, he shows that isolating pseudoscience from virtuous science is not so easy after all:
We may disagree on some of the likely borderline cases. For instance, is SETI, the Search for Extraterrestrial Intelligence, a pseudoscience? I’d say no, but I would understand why someone might have doubts. What about parapsychology? I’d say yes, it is a pseudoscience, but, again, there may be room for disagreement.
One is tempted to wonder whether “room for disagreement” is a polite term for Not Yet Cancelled. But Pigliucci goes on to say something quite interesting: the question is much more fraught than the policing of “borderline cases” would suggest.
Whom Should We Trust?
He cites a 2023 paper by fellow philosopher Kåre Letrud of Inland Norway University of Applied Sciences. Letrud was trying to determine how consistently a discipline was labelled as pseudoscience. According to his Abstract, he found “inconclusive evidence for an overall agreement,” adding “However, the frequent usage of a small number of pseudoscience-cases indicates that these are considered paradigms of pseudoscience. ”
Pigliucci comments
The consensus cases were not unexpected: astrology, creationism, homeopathy, intelligent design, parapsychology, and UFOs. The situation was less clear for alternative medicine, ancient astronauts, climate change denialism, and several others. And there was almost no apparent consensus for a long list, including animal magnetism, the anthropic principle, anti-gravitational devices, the Bermuda Triangle, Feng Shui, cell phone radiation, and on and on.
MASSIMO PIGLIUCCI, “PSEUDOSCIENCE: DO WE KNOW WHAT WE ARE TALKING ABOUT?,” SKEPTICAL INQUIRER, JULY/AUGUST 2024
He adds,
This is more than somewhat unexpected. If you go through the list presented by Letrud as a multi-page bar graph and available as a spreadsheet in the supplementary materials accompanying the paper, you might be surprised at so many (to me!) obvious examples of pseudoscience, including several of those I just listed, that didn’t make the cut.
PIGLIUCCI, “WHAT WE ARE TALKING ABOUT?”
Nonplussed, Pigliucci suggests ignoring the slender philosophical literature on the topic and focusing on work published in — reader, are you ready for this? — Skeptical Inquirer itself!
The best source of serious writing on pseudoscience, I suggest, are the few magazines dedicated to the topic and published by organizations that are focused on the phenomenon, such as Skeptical Inquirer. Skeptics are the professionals, in this case, not scientists or philosophers, except for those very few philosophers of science who work specifically on pseudoscience, such as yours truly.
PIGLIUCCI, “WHAT WE ARE TALKING ABOUT?”
And the philosophy world should also defer to his opinion — the modest opinion of a philosopher who accepts neither the independent existence of the mind nor free will.
As we noted recently, his pronouncements on these topics do not follow from any dramatic new science findings:
As a matter of fact, earlier this year David Chalmers, the very same non-materialist philosopher that Pigliucci was excoriating in that passage in his essay, won the famous 25-year bet with neuroscientist Christof Koch. In that agreed-on period, Koch was was unable to find the “consciousness spot” in the brain. It is definitely intellectual pressure, not achievement, that keeps materialism strong in the neurosciences.
What Role Does Evidence Play?
If there are criteria that demarcate science from pseudoscience, we might expect evidence to play a strong role. But evidence is not likely to be dealt with even-handedly in an environment riddled with strong philosophical (and perhaps sometimes political) commitments. To take one example, the vast evidence for fine-tuning of our universe for life would seem to imply some sort of underlying design. Yet, without blinking, otherwise intelligent people will retort, “That just shows that there are countless universes out there!”
We have evidence for the design of our universe but no evidence for the countless other universes. The decision to prefer what we don’t see to what we do see is not based on weighing evidence but on philosophical preference. And philosophical preference drives efforts to identify threatening patterns of evidence — for example, intelligent design — as pseudoscience.
Overall, it’s no wonder that few philosophers write on the topic of pseudoscience. Speaking of Skeptical Inquirers, perhaps we should be much more skeptical of the whole concept of pseudoscience, at least as it plays out now. If there is evidence for a phenomenon in nature, we can attempt to evaluate that evidence (or lack thereof) without using a label that mainly serves the interests of naturalist (materialist) atheism. Worse, use of the label elevates that perspective to the position of — an entirely undeserving — public referee of science.
Tuesday, 2 July 2024
Monday, 1 July 2024
Primeval nanotech vs. Darwin.
Scientist Discovers a Protist’s “Cellular Origami” — The First Known Case
Sometimes evidence for design is subtle and arcane, discernible only through careful logic and mathematical analysis.
At other times, the exquisite design of life just seems to hit you over the head. That’s how I felt when I saw the cover illustration for the June issue of Science. The illustration depicts the single-celled protist Lacrymaria olor in a state of expansion and a state of contraction: the first ever known case of “cellular origami.”
The discovery came from the lab of Stanford’s Manu Prakash, who spent seven years uncovering the folding/unfolding mechanism. Stanford Report does a good job describing the mesmerizing beauty of it:
…a single teardrop-shaped cell swims in a droplet of pond water. In an instant, a long, thin “neck” projects out from the bulbous lower end. And it keeps going. And going. Then, just as quickly, the neck retracts back, as if nothing had happened.
In seconds, a cell that was just 40 microns tip-to-tail sprouted a neck that extended 1500 microns or more out into the world. It is the equivalent of a 6-foot human projecting its head more than 200 feet. All from a cell without a nervous system.
This “incredibly complex behavior,” as Dr. Prakash says, is derived from literal origami. The structure of the cell membrane is folded in a “curved crease origami” style that allows it to extend and retract consistently — 50,000 times in the lifetime of a protist, without any errors.
Destined for Origami?
Origami seems to be following Dr. Prakash. As chance would have it, before he discovered the origami of Lacrymaria olor, he had already used origami in his own engineering designs. (Or maybe his experience with origami made him ready to recognize it when he encountered it in nature?) Prakash invented an origami microscope, dubbed a “foldscope,” that costs only $1.75 to produce. In 2014, he mailed 50,000 foldscopes to recipients all around the world. His aim was to inspire and empower people to begin doing science in far-flung places where expensive and unwieldly lab equipment is impractical. A New Yorker piece lists some delightful outcomes of his project:
A plant pathologist in Rwanda uses the Foldscope to study fungi afflicting banana crops. Maasai children in Tanzania examine bovine dung for parasites. An entomologist in the Peruvian Amazon has happened upon an unidentified species of mite. One man catalogues pollen; another tracks his dog’s menstrual cycle.
A few years back, Prakash himself used his invention to discover a different amazing design feature in nature. He was looking at marsh water through his foldscope when he witnessed a single-celled Spirostomum suddenly contract to a fraction of its original size. Prakash discovered that Spirostomum are able to contract in response to danger in just 5 milliseconds, and the resulting ripples in the water trigger other nearby Spirostomum cells to do the same in a rapid domino effect — a previously undiscovered form of intercellular communication.
Biology and Engineering
You will probably not be surprised to hear that Dr. Prakash is an engineer as well as a biologist. This is predictable, because engineers tend to have a design-oriented mindset that is very well suited to discovering the design plans of living organisms. Prakash and his lab attack biology problems like engineers studying the artifacts of a more advanced civilization, tracking the tiniest movements of microbes in the lab to uncover the underlying mechanisms that enables them to function the way they do.
So it’s also not surprising that Prakash is dreaming of design applications for what he’s seen in Lacrymaria olor. Prakash thinks that tiny machines based on the design of Lacrymaria olor could be used for telescopes and surgical robots, among other applications.
It wouldn’t be the first time Prakash has copied ideas from life. According to the New Yorker piece, Prakash molds the lenses of his foldscopes using a device he created based on the beak of a red-necked phalarope, a bird that moves its beak in a “rapid tweezing motion” to mold droplets of food and water into aspherical shapes before swallowing them.
Life and Art
It’s a never-ending story: engineers uncover the engineering of nature by drawing analogies to human feats of engineering, and what they see in nature inspires them to engineer new innovations, which are used to uncover new engineering features in nature…and on and on.
Art imitates life, and life imitates art, and at some point the distinction between the two becomes blurry. Where does one end and the other begin?
Maybe the line is imaginary. To call the structure of Lacrymaria olor “origami” is not merely to draw a comparison — it really is origami. In fact, when Prakash and his team refer to it as “curved crease origami,” they are referring to a specific type of origami that originated in the Bauhaus art school in Germany in the late 1920s.
Little did those German origamists know, they’d been beaten to the punch. Oh, well. Perhaps the best any human artist can do is imitate the Greater Artist.
Intelligent Design 101
Introduction to the Scientific Theory of Intelligent Design
Author’s note: This introductory article on intelligent design first appeared June 19 in Polish at Fundacja En Arche’s ID Website
To understand the origins of the modern intelligent design movement, you must first understand that Darwin’s implausible explanation for evolution has become more and more implausible with every new biological and biochemical discovery, and that there never has been a plausible natural explanation for the origin of life on Earth. Here are some useful places to start, to understand this. One is this Article by David Klinghoffer which reviews a June 2022 article in The Guardian entitled “Do we need a new theory of evolution?” My own 2000 opinion piece in The Mathematical Intelligencer, “A Mathematician’s View of Evolution,” and the video “Why Evolution Is Different,” may also be useful.
The second thing you need to understand is that for many years the scientific establishment has insisted that no matter how implausible Darwin’s explanation might have become, the alternative of design cannot be considered because it is a religious idea. And for many years, most public challenges to Darwinism were in fact attempts to force science to fit a literal interpretation of the early chapters of Genesis. In the first creation-evolution debate I ever attended, in the 1970s, the creationist spent much of his time arguing for a young Earth, as though that were the main issue.
Good Logic, Good Science
But toward the end of the last century a few scientists (biochemist Michael Behe and geneticist Wolf-Ekkehard Lӧnnig, for example) began to argue that it has become so obvious that life cannot be explained without design that “intelligent design” has to finally be taken seriously in the scientific world. While other religious beliefs based on the Bible or our experience or intuition may not be science, the conclusion that there must be a designer behind living things is just good logic and thus good science, even if science alone cannot tell us who designed life, or how. If scientists can spend time and money developing tools and algorithms to detect dubious signs of extraterrestrial intelligence in weak signals from outer space, why are they required to ignore the evidence in living cells where design practically leaps out at you?
Evolution Is Different
Of course, normally if a scientific theory for some observed phenomenon fails, we just look for an alternative “natural” theory. But what has long been obvious to the layman is finally becoming clear to many scientists, that evolution is different. We are not talking now about explaining earthquakes or comets or volcanos, we are talking about explaining hearts and lungs and eyes and ears. How many theories without design can there be for the origin of circulatory systems, nervous systems, and human brains? Design has finally started to be taken seriously by scientists not because there are minor problems with Darwin’s explanation, but because it has become absurdly, blindingly obvious that neither it nor any other theory that ignores design will ever completely explain living things. Contrary to common belief, science really has no reasonable alternative to design to explain either the origin or evolution of life. In fact, we really have no idea how living things are able to pass their current complex structures on to their descendants without significant degradation, generation after generation, much less how they evolve even more complex structures.
If you look closely, you will notice that all the most persuasive arguments used to reject design are not of the form “here is a reasonable theory on how it could have happened without design” but rather “this doesn’t look like the way God would have done things,” an argument used frequently by Darwin himself. In the debate I mentioned earlier, the evolutionist spent much of his time showing dozens of beetle species, sarcastically concluding “God must really like beetles.” Well, I’ll admit I might not have predicted God would design so many species of beetles and there are other things about the history of life on Earth — the long times involved, for example — that to our minds seem to suggest natural causes, but no clue as to how it could have all happened without design.
In the 2000 Mathematical Intelligencer piece (highlighted in the video “A Mathematician’s View of Evolution”) I compared the history of my partial differential equation software to the history of life, noting that there are large jumps in both where major new features appear, for the same reasons: gradual development of the new organs or new systems of organs that gave rise to new orders, classes, and phyla would require the development of new but not yet useful features. So, Darwinism could not explain the development of these new features even if they did occur gradually — and, according to the fossil record, they don’t. But I have always felt that the strongest argument for design is simply to state clearly what you have to believe to NOT believe in intelligent design, and I closed the article with this:
I imagine visiting the Earth when it was young and returning now to find highways with automobiles on them, airports with jet airplanes, and tall buildings full of complicated equipment, such as televisions, telephones and computers. Then I imagine the construction of a gigantic computer model which starts with the initial conditions on Earth 4 billion years ago and tries to simulate the effects that the four known forces of physics (the gravitational, electromagnetic and strong and weak nuclear forces) would have on every atom and every subatomic particle on our planet (perhaps using random number generators to model quantum uncertainties!).
If we ran such a simulation out to the present day, would it predict that the basic forces of Nature would reorganize the basic particles of Nature into libraries full of encyclopedias, science texts and novels, nuclear power plants, aircraft carriers with supersonic jets parked on deck, and computers connected to laser printers, CRTs, and keyboards? If we graphically displayed the positions of the atoms at the end of the simulation, would we find that cars and trucks had formed, or that supercomputers had arisen? Certainly we would not, and I do not believe that adding sunlight to the model would help much. Clearly something extremely improbable has happened here on our planet, with the origin and development of life, and especially with the development of human consciousness and creativity.
Not a Real Physical Force
Of course, constructing such a model is impossible, but I thought imagining it was a useful exercise to get across the point that natural selection, the one unintelligent force in the universe widely credited with the ability to create spectacular order out of disorder, is not a real physical force and cannot be included in the simulation, and the point that unintelligent forces cannot explain human intelligence. Rice University chemist James Tour makes a similar point regarding the origin of life: “Molecules don’t care about life.”
Furthermore, even many of the scientists who insist that everything must be explained in terms of the unintelligent laws of nature alone have been forced by the evidence uncovered in the last half century to accept that design is required to explain the spectacular fine-tuning for life of the laws and constants of physics themselves. These scientists are sometimes considered to be intelligent design supporters as well. One of the three discoveries discussed in Stephen Meyer’s book Return of the God Hypothesis: Three Scientific Discoveries that Reveal the Mind Behind the Universe is this well-documented fine-tuning. Notice the long list of distinguished scientists who have formally endorsed the book, including physics Nobel Prize-winner Brian Josephson who writes, “This book makes it clear that far from being an unscientific claim, intelligent design is valid science.”
Sunday, 30 June 2024
Human devolution?
Neanderthals Cared for Down Syndrome Children
Scientists have discovered the remains of a Neanderthal child with Down syndrome. From the Guardian story:
The survival of this child, beyond the period of breastfeeding, implies group caregiving, probably more extended than parental caregiving, typical of a highly collaborative social context among the members of the group. Otherwise, it is very difficult to explain the survival of this individual up to the age of six years,” said Valentín Villaverde, a co-author of the study and an emeritus professor of prehistory at the University of Valencia.
Conde-Valverde said: “The discovery of Tina represents the oldest known case of Down’s syndrome and demonstrates that the diversity observed in modern humans was already present in prehistoric times. This finding ensures that the story of human evolution includes us all.”
Consequences of “Enlightenment”
Such compassion is on the outs in these “enlightened” days. Indeed, it may now be that more babies with Down syndrome are killed in the womb than are born. Indeed, countries such as Iceland have all but eliminated citizens with Down syndrome via prenatal testing and almost universal terminations. Denmark, too.
In the U.S., the numbers are tricky. Some studies claim that the majority of such babies are terminated during gestation. But even if the actual rate is lower, at the very least, the number of people with Down syndrome has been reduced by at least 30 percent with the advent of prenatal testing. And often, genetic counselors push the termination option. Peter Singer argues that if such babies are born, parents should be allowed to have them killed — and yet, despite this bigotry, he is the most celebrated bioethicist in the world.
What a tragedy for these dead precious babies and for us. Perhaps we could learn something from our ancient relatives.
Yet more preDarwinian design vs. Darwinism.
“Irreducible Complexity” May Be Part of the Definition of Life
There are many bad counter-arguments to Michael Behe’s famous irreducible complexity conundrum, and (in my opinion) one pretty good one.
For those unfamiliar with Behe’s argument, it goes like this:
Darwinian evolution is supposed to build complex systems gradually, overcoming vast improbabilities in tiny steps over billions of years. But, strangely, many systems in living organisms are “irreducibly complex” — they contain a core set of key elements that are all absolutely necessary for the system to function at all. Gradual evolution through random variation and natural selection could never build such a system, because the system would have no adaptive function until it was already completely finished.
After Behe made this case in his 1996 book Darwin’s Black Box, scientists (and non-scientists) scrambled to rebut him. Some argued that the systems in question weren’t really irreducibly complex; others, that they could have arisen through cooption of parts from other systems; others, that they emerged as reductions from larger complex systems that were not irreducibly complex… and so on.
None of those arguments have held up to logical or empirical scrutiny. But I don’t think those argument are the real reason that most who find Behe’s argument unpersuasive find it unpersuasive. I suspect that the real objection for most people is something more gut-level and foundational, which might be expressed something like this:
Okay, so maybe it’s hard to see how gradual, blind processes could produce a few special systems like the bacterial flagella. Because of irreducible complexity — got it. But Darwin’s theory still makes sense for everything else. So are we really going to throw out the whole theory on the basis of a few things we can’t explain? Isn’t it more likely that there’s some explanation for these things, and we just have to wait for it?1
After all, if Darwinian evolution works in theory, then it seems to follow that Darwinian evolution should have happened. And then, if living organism don’t look like they were made by Darwinian evolution, the question just becomes, “So where the heck are the things that were made by Darwinian evolution?” Even if the presence of irreducible complexity shows that all the organisms we study didn’t arise by Darwinian evolution, it doesn’t explain why they didn’t arise by Darwinian evolution.
Confusion and Mystery
In other words, for the irreducible complexity argument to persuade someone away from Darwinism, it’s not enough to show that some structures in living organisms don’t look like they were made from unguided Darwinian processes. As long as unguided Darwinian processes work in theory, the existence of irreducibly complexity in life may add confusion and mystery, but it doesn’t do away with the theory. For the argument to be really convincing, you need to also show that Darwinism doesn’t actually work to construct living organisms even in theory.
Might this be the case? Well, it would be the case if irreducible complexity is actually necessary for living systems. If something needs to be irreducibly complex in order to achieve the characteristics that would make us call it “alive,” then Darwin’s theory doesn’t even work in theory, and the mystery is solved — we see features that Darwinian evolution can’t explain simply because Darwinian evolution didn’t actually happen, and can’t happen.
Behe argued something like this in response to the criticisms of his first book. But it was at first an open question — there is no quick-and-easy way to tell if irreducible complexity is intrinsic and necessary to life, or not.
It’s extremely interesting, then, that the prominent theoretical biologist Stuart Kauffman has been promoting a definition of life that entails irreducible complexity — though Kauffman (who is unsympathetic towards ID) doesn’t use that term.
A Definition of Life
Kauffman has been arguing that what sets living organisms apart from non-living things, and what makes them able to function and to evolve, is that in living organisms the parts exist for and by means of the whole. Kauffman calls such systems “Kantian wholes” (because the idea comes from Immanuel Kant’s Critique of Judgement). A Kantian whole, to put it another way, is a self-creating system in which everything supports and depends upon everything else.
It’s easy to see how living organisms fit this definition. Your various parts can’t exist without you — you’ll never find a brain or a spleen lying around on its own (at least, not for very long). Likewise, you wouldn’t exist if you didn’t have those parts (at least, not for very long).
It’s also easy to see that such a system is by definition irreducible complex. The “whole” — by definition — encompasses all of the parts. So, if the whole is necessary for the continued existence of the parts, then all of the parts are necessary for the continued existence of the parts — which is the definition of irreducible complexity. Not all irreducibly complex systems are necessarily Kantian wholes, but Kantian wholes are necessarily irreducibly complex.
Irreducible Complexity in LUCA
Of course, someone will probably point out that this is all very interesting philosophizing, but science is about empirical evidence. And Kauffman, as a scientist, is eager to provide it. To this end, he co-authored (with the up-and-coming origin of life researcher Joana Xavier and others) a paper published in Proceedings of the Royal Society B which seemed to show that life has existed in the form of Kantian wholes as far back in evolutionary history as we can see.
Xavier et al. took a database of metabolic reactions in bacteria and archaea (the two domains of the simplest lifeforms) and looked at which reactions they had in common. They found in the intersection of bacteria and archaea a collectively autocatalytic set of 172 reactions. (“Collectively autocatalytic” means that the set of reactions is self-creating — all the catalysts of the reactions in the set are created by other reactions in the same set; e.g. A creates B, B creates C, C creates A.) From a phylogenetic perspective, this implies that the common ancestor of bacteria and archaea — and thus presumably the “last universal common ancestor” (LUCA) itself — was characterized by complex autocatalytic metabolic cycles. In a paper in the volume Evolution “On Purpose”: Teleonomy in Living Systems, Kauffman and his colleague Andrea Roli write that these findings “very strongly suggest that life arose as small-molecule collectively autocatalytic sets.”
Kauffman and his co-theorists believe that collectively auto-catalytic sets are Kantian wholes. Therefore, they argue that life has been characterized by Kantian whole-ness from the very beginning, in accordance with Kauffman’s contention that living things are Kantian wholes by their very nature. If that’s true, then — as we have seen — that means that life, by its very nature, is irreducibly complex.
What Was the Question?
If irreducible complexity really is part of the definition of life, this solves the problem raised in the response to Behe’s irreducible complexity argument.
It all comes down to What is it that we’re trying to explain? when we invoke evolution or design. Why does life need an explanation at all? What is it that makes people, cows, mushroom, pine trees, bacteria, and so forth, so very perplexing to us?
Darwin seemed to think the problem was mere complexity, or the adapted-ness of organisms to their environment. That seems plausible at first glance, but in retrospect we should have known that it isn’t the case. A pile of sand is complex — the odds of obtaining that exact same arrangement of grains of sand a second time are almost nil — but nobody thinks that the existence of piles of sand is some big mystery.
No, the thing that makes living organisms so mysterious (one of the things that makes them mysterious, anyway) is that they are irreducibly complex: they move, act, reproduce, and grow by means of an elaborate system of interconnected, interworking parts. It’s obvious (with 20-20 hindsight) that this is the real mystery in need of explanation, and it’s equally obvious that the ability of natural selection to pile up tiny, individually useful random variations in no way explains (or even attempts to explain) how such an intricate network could come to be.
So when Behe pointed to irreducible complexity, he wasn’t noticing some random, inexplicable feature of certain biological systems and using it to attack Darwin’s theory. Rather, he was putting his finger on what exactly it is about life that makes us feel it needs explaining. And that turned out to be something about which Darwin’s insights, brilliant though they were, had nothing to say.
Notes
For example, this line of thinking has got to be why evolutionary biologist Bret Weinstein feels that “if we pursue that question [a particular problem raised by ID proponents], what we’re going to find is, oh, there’s a layer of Darwinism we didn’t get and it’s going to turn out that the intelligent design folks are going to be wrong” — even though he admits that ID proponents are pointing to genuine holes in the current theory of evolution.
Saturday, 29 June 2024
Yet another of the fossil records many big bangs.
Fossil Friday: Snake Origins —Yet Another Biological Big Bang
This Fossil Friday features the “legged” snake Najash rionegrina from the Late Cretaceous of Patagonia, which is one of the oldest fossil snakes known to science. It was found in terrestrial sediments and shows a well-defined sacrum with pelvis connected to the spine and functional hind legs. Therefore it was considered as supporting an origin of snakes from burrowing rather than aquatic ancestors (Groshong 2006). I had reported about the highly controversial and hotly debated topic of snake origins in a previous article (Bechly 2023), where you can find links to all the relevant scientific literature.
Another Open Question
But there was another open question concerning the origin of snakes: Did their distinct body plan evolve gradually as predicted by Darwinian evolution, or did snakes appear abruptly on the scene as predicted by intelligent design theory? Earlier this year a seminal new study was published by a team of researchers from the University of Michigan and Stony Brook University in the prestigious journal Science (Title et al. 2024). This study brought important new insights with the mathematical and statistical modelling of the most comprehensive evolutionary tree of snakes and lizards, based on a comparative analysis of the traits of 60,000 museum specimens and the partial sequencing of the genomes of 1,000 species (SBU 2024, Osborne 2024). The study found that all the characteristic traits of the snake body plan, such as the flexible skull with articulated jaws, the loss of limbs, and the elongated body with hundreds of vertebrae, all appeared in a short window of time about 100-110 million years ago (Rapp Learn 2024).
The authors commented in the press releases that this burst of biological novelty suggests that “snakes are like the Big Bang ‘singularity’ in cosmology” (SBU 2024; also see Cosmos 2024,Osborne 2024, Sivasubbu & Scaria 2024, Wilcox 2024). This arguably would imply that snakes became “evolutionary winners” because they evolved “in breakneck pace” (Wilcox 2024), which the senior author of the study explained with the ad hoc hypothesis that “snakes have an evolutionary clock that ticks a lot faster than many other groups of animals, allowing them to diversify and evolve at super quick speeds” (Osborne 2024). Well, that is not an explanation at all, but just a rephrasing of the problem. How could such a super quick evolution be accommodated within the framework of Darwinian population genetics and thus overcome the waiting time problem? After all, the complex re-engineering of a body plan requires coordinated mutations that need time to occur and spread in an ancestral population. Did anybody bother to do the actual math to check if such a proposed supercharged evolution is even feasible, given the available window of time and reasonable parameters for mutation rates, effective population sizes, and generation turnover rates? Of course not. We just have the usual sweeping generalizations and fancy just-so stories.
The Fatal Waiting Time Problem
My prediction is that this will prove to be another good example of the fatal waiting time problem for neo-Darwinism. In any case we can add the origin of snakes to the large number of abrupt appearances in the history of life (Bechly 2024), and I am happy to embrace the name coined by the authors of the new study for this remarkable event: The macroevolutionary singularity of snakes. This does not sound very Darwinian, does it? So what do the authors suggest as causal explanation? They have none and the press release from Stony Brook University (SBU 2024) therefore concludes with this remarkable admission: “The authors note that the ultimate causes, or triggers, of adaptive radiations is a major mystery in biology. In the case of snakes, it’s likely there were multiple contributing factors, and it may never be possible to fully define each factor and their role in this unique evolutionary process.” It other words, it was a biological Big Bang and they have no clue what caused it. But of course it must have been unguided evolution, no intelligence allowed!
References
- Bechly G 2023. Fossil Friday: Is the Four-Legged Snake Tetrapodophis a Missing Link or Not? Evolution News December 22, 2023. https://evolutionnews.org/2023/12/fossil-friday-is-the-four-legged-snake-tetrapodophis-a-missing-link-or-not/
- Bechly G 2024. Fossil Friday: Discontinuities in the Fossil Record — A Problem for Neo-Darwinism. Evolution News May 10, 2024. https://evolutionnews.org/2024/05/fossil-friday-discontinuities-in-the-fossil-record-a-problem-for-neo-darwinism/
- Cosmos 2024. The secret behind snakes’ evolutionary success is speed. Cosmos February 25, 2024. https://cosmosmagazine.com/news/the-secret-behind-snakes-evolutionary-success-is-speed/
- Groshong K 2006. Oldest snake fossil shows a bit of leg. NewScientist April 19, 2006. https://www.newscientist.com/article/dn9020-oldest-snake-fossil-shows-a-bit-of-leg/
- Osborne H 2024. Snakes are built to evolve at incredible speeds, and scientists aren’t sure why. LiveScience February 22, 2024. https://www.livescience.com/animals/snakes/snakes-are-built-to-evolve-at-incredible-speeds-and-scientists-arent-sure-why
- Rapp Learn J 2024. 100 Million Years Ago Snakes Gained Their Most Iconic Traits. Discover Magazine June 4, 2024. https://www.discovermagazine.com/planet-earth/100-million-years-ago-snakes-gained-their-most-iconic-traits
- SBU 2024. Snakes: An Evolutionary Winner. Stony Brook University News February 22, 2024. https://news.stonybrook.edu/newsroom/press-release/general/snakes-an-evolutionary-winner/
- Sivasubbu S & Scaria V 2024. In snake genes, study finds they evolved 3x faster than other reptiles. The Hindu March 3, 2024. https://www.thehindu.com/sci-tech/science/singularity-of-snakes-evolution-burst-genetics/article67909956.ece
- Title PO, Singhal S, Grundler MC et al. 2024. The macroevolutionary singularity of snakes. Science 383(6685), 918–923. DOI: https://doi.org/10.1126/science.adh2449
- Wilcox C 2024. Snakes are ‘winning’ at evolution. ScienceAdviser February 23, 2024. https://www.science.org/content/article/scienceadviser-snakes-are-winning-evolution
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