Wednesday 14 August 2024
Monday 12 August 2024
Madness in the method?
An Object Lesson in How Not to Do Science
British science writer Philip Ball, looks back on the mapping of the human genome and what has followed from it. Writing at Aeon, he senses a need for change in the way we look at Earth’s life forms. But he doesn’t seem to want too much change.
As the author of How Life Works (University of Chicago Press 2023) and Beautiful Experiments (University of Chicago Press 2023), Ball admits,
Talk of a genetic blueprint, of selfish genes, of instruction books and digital codes gave us a narrative we could grasp. Even though we now know this to be at best a partial and at worst a misleading picture, it’s likely to remain in place until there is something better on offer.
PHILIP BALL, “WE ARE NOT MACHINES,” AEON, JULY 12, 2024
What Most of Us Learned in School Was Faulty
He is aware of the limitations of that point of view but sees it as part of the inherent conservatism of science. Still, he looks for another, more accurate story. Thus, he reveals — surprising many of us perhaps — that most of what we learn in school gives rise to misconceptions. For example,
Only around 1-2 percent of the entire human genome actually consists of protein-coding genes. The remainder was long thought to be mostly junk: meaningless sequences accumulated over the course of evolution. But at least some of that non-coding genome is now known to be involved in regulating genes: altering, activating or suppressing their transcription into RNA and translation into proteins. Many disease-linked regions are in these regulatory sequences, where mutations don’t change the proteins themselves but, rather, the rate or chance of them being made at all. So, to understand how life really works at the genomic level, we need to understand gene regulation. And that, as we’ll see, is not just eye-wateringly complicated but not at all what we have learnt to expect from the conventional molecular biology of the past 50 years.
BALL, “WE ARE NOT MACHINES”
And not all genes even encode proteins. Also RNA seems to have some functions other than serving as a messenger for making proteins.
Ball grasps the strangeness of the fact that the public still hears the same Central Dogma story about the human genome as it did in the 1960s and thus has little idea how complex it all really is — and how poorly understood:
Thetemptation is to throw up one’s hands and conclude that, for humans at least, how life works surpasses all understanding. Some biologists have implied as much, suggesting that we might never truly understand life mechanistically, but will just have to rely on data mining with black-box AI to make predictions about what will lead to what.
BALL, “WE ARE NOT MACHINES”
Leaving it all to the computer does not, of course, seem like an obviously sound idea. And Ball goes on to say something quite profound:
… it’s not hard to see why, the more complex the organism, the fuzzier its molecular mechanisms have to be. A huge machine that works only if all its countless components interlock in precisely coordinated ways is far too fragile —especially if those parts are, like molecules, constantly moving about randomly in a warm, wet environment. By the same token, if life relied on the accurate readout of innumerable genomic instructions in exactly the right order, it would be far too vulnerable to errors. It’s for these reasons that we are not machines — not, that is, like any machine humans have ever built. It’s a far better and more robust solution to find principles that work over many hierarchical levels, with the operation at one level being not too sensitive to the fine details of the levels below. Gene regulation by rather loosely defined condensates rather than by specific molecular switches, say, means that it can still work without every molecule having to be present and correct.
BALL, “WE ARE NOT MACHINES”
Yes But how is this astonishing feat accomplished?
Evolution has, to speak anthropomorphically, evidently ‘designed’ our molecules to work in this fuzzy way. In contrast to the lock-and-key principle by which protein enzymes were long thought to recognise and transform their target molecules, some of the most important proteins in our cells, including many transcription factors, have shapes that are only loosely defined, enabling them to stick to others without being too choosy about it. And those little regulatory RNAs are generally too small to carry enough information for their unions to be very selective; they too work collectively, arriving at a decision, as it were, by committee.
BALL, “WE ARE NOT MACHINES”
The Unthinkable Thought
In short, the life we know can only be envisioned by appealing to intelligent design, while pretending not to.
Ball goes on to address the question of why the problems with the current picture are not better known: “Having long interacted with scientists of all persuasions, I’ve noticed a contrast between how physicists and biologists receive and communicate new ideas.”
Oh for heaven’s sakes, why can’t he just come right out and admit the reality? There is no reasonable hope that Darwinian evolution could have done all that is required in the time allowed — or in any amount of time. And, given how much has been invested in Darwinism over the years, no one wants to be first to stick a trowel in that beehive. That’s why.
Ball goes on to discuss the ENCODE project, which found that supposedly “junk DNA” often does have a biological function:
Some biologists responded by saying, in effect: ‘No no no, nothing to see here – our existing understanding is just fine.’ (This was mild stuff compared with the furious reaction the ENCODE paper itself elicited from some biologists, who accused the team of evolutionary heresy on a par with intelligent design.) Others said that, even if biology was indeed more complicated that we’d thought, what was to be gained by telling the public that? In other words: don’t upset the status quo.
BALL, “WE ARE NOT MACHINES”
Investment in a Belief System
That’s not about science; it’s about investment in a belief system. When Ball, admirably, checked the story out in the Systems Biology department at Harvard one summer, he learned that the whole thing was “much worse than that!” He now thinks that biologists are too invested in the Human Genome Project approach and that we need “new narratives” in biology. But then he also argues,
It has also become much harder in recent years for scientists to admit to gaps in knowledge and understanding, which will be exploited by everyone ranging from creationists to climate-change deniers to anti-vaxxers as evidence that we shouldn’t believe a word they say.
BALL, “WE ARE NOT MACHINES”
In short, the story the public is told is contrary to evidence — and to reason, actually — but scientists have to keep telling it because otherwise the wrong people might benefit. That is practically an object lesson in how not to do science. But Ball has thought and said as much as he can while remaining safe.
Sunday 11 August 2024
Saturday 10 August 2024
Darwinism can't spin straw into gold?
How “Junk” DNA Got Its Function: Evolutionary Tales Fail to Convince
Recently I wrote about various functions that have been identified for “junk” DNA. Of course, many functions have been discovered for the supposed “junk,” but these form a special case where diseases played a role. How are they being identified? It’s because when those functions go wrong, diseases result. Most evolutionists aren’t bothered by such findings of individual functions for junk DNA. They just claim that occasionally junk gets co-opted to do something useful, or even vital to our health. They offer evolutionary accounts of how the junk got its function — but those accounts often appear highly unlikely. Here are a couple of examples.
Did junk DNA cause humans to lose their tails.
Earlier this year there was a flurry of stories about how “junk DNA” may explain why humans don’t have tails. As the story goes, a transposable element called an Alu sequence got randomly inserted into a regulatory intron of a gene called TBXT, which is involved in the early development of the neural tube (which later becomes the spinal column). An evolutionary story ensues, outlined at Study Finds:
The researchers identified a specific genetic alteration — an inserted piece of DNA — present in humans and apes but absent in monkeys. This insertion, located in a gene known as TBXT, is believed to play a critical role in the development, or rather the absence, of tails in humans.
Technical paper in Nature elaborates on the story.
We demonstrate that this Alu element — inserted into an intron of the TBXT gene — pairs with a neighbouring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. … the exon-skipped transcript is sufficient to induce a tail-loss phenotype.
This particular Alu element is precisely located to allow the gene variant to arise — as the study’s lead author tweeted:
So it takes TWO to make an impact! The unique alignment of a pair of Alu elements is crucial; without it, neither element would have significance.
One scientist called this event a “strange evolutionary quirk.” Strange indeed. The story is an evolutionary framing of the study’s findings, and it’s cool research, but what is the raw data here? The raw data is simply a genetic difference that has been identified between hominoids and monkeys, and the difference is likely part of what builds the tail-less hominoid body plan. The evolutionary story thus makes a common mistake: it confuses the identification of how some aspect of human development works with an evolutionary explanation of how that aspect of the body plan originated.
Moreover, if this were a true evolutionary story, it’s doubtful that the change alone really would be “sufficient” to cause an advantageous change leading to tail-loss. The technical paper suggests other mutations were probably needed:
[E]ven if the AluY insertion substantially influenced tail-loss evolution in hominoids, additional genetic changes may have acted to stabilize the no-tail phenotype. Such possible hominoid-specific variants in tail-development-related genes may have preexisted in the ancestral genome or occurred after the AluY insertion. Such a possible set of genetic events suggest that a change to the AluY element in modern hominoids would be unlikely to result in the reappearance of the tail.
The technical paper reports that when this gene variant is induced in mice, “mice expressing the exon-skipped Tbxt isoform develop neural tube defects.” Humans can experience this genetic defect as well, and this means that undoubtedly multiple coordinated genetic changes would have been necessary to evolve the tail-less phenotype without experiencing other disease-related problems, such as neural tube defects. The paper continues:
We suggest, however, that the selective advantage must have been strong because the loss of the tail may have included an evolutionary trade-off of neural tube defects, as demonstrated by the presence of neural-tube-closure defects in mice expressing the TbxtΔexon6 transcript.
The language there is interesting: because of the highly deleterious neural-tube closure defects associated with this gene variant in mice, the only way this could change could have been selected was if it provided a “strong” selective advantage offsetting the greatly increased likelihood of disease — an “evolutionary trade-off.” It’s hard to imagine a scenario where such a greatly increased risk of disease would somehow be tolerable simply in exchange for losing your tail. Multiple other coordinated mutations would seemingly be needed to avoid serious birth defects. But when multiple mutations are needed to avoid such deleterious defects, that is highly unlikely under blind evolution and speaks to the need for foresight, planning, and intelligence.
Interestingly, a co-author of the study noted in Scientific American that this evidence shows that Alu sequences “aren’t just cluttering the genome” and are “important”
AluY was an unexpected piece of the puzzle because millions of such elements are present in our cells — and for a long time they were referred to as “junk DNA” because researchers believed they were littering the human genome at random and seemingly with no purpose. “It shows that these elements aren’t just cluttering the genome,” Yanai says. “They’re doing something important.”
Taken as a whole, this tale provides more evidence that when you mess with the “junk,” you mess with its function, and problems arise. And evolutionary stories of how the junk got its function just aren’t adding up. If this story were true, then multiple mutations would be necessary in order to avoid very severe developmental defects, something that points to planning and design, not blind evolution.
Does Junk Give Us Big Brains?
Here’s another example of a questionable evolutionary story about how junk DNA got its function: An article at Live Science says “Humans’ big-brain genes may have come from ‘junk DNA.’” They report, “the genes that enabled human brains to grow large lobes and complex information networks may have originally emerged from junk DNA.” Once again, identifying how things work is not an explanation for how they evolved. The original paper in Nature Ecology & Evolution states:
Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear.
Don’t miss the words “all-or-nothing transition” — this suggests that transforming the “junk” into functional genes would have required many coordinated changes. Sure, these genes are important for human brain development, but is such a set of coordinated changes to transform “junk” into crucial genes likely to occur by blind evolution? It seems not.
Whatever the answer, this much is clear: junk DNA performs many important functions, and when evolutionists try to interpret the origins of those functions from within their paradigm, the results often fail to stand up to scrutiny.
Friday 9 August 2024
An air strike against Darwinian gradualism?
Fossil Friday: The Carboniferous Explosion of Winged Insects
Among the numerous abrupt appearances of new animal body plans in the history of life (Bechly 2024) there are also striking examples from my own field of research, which is the fossil history of winged insects (Pterygota), the most diverse group of organisms which includes more described species than all other multicellular life combined (Grimaldi & Engel 2005). Therefore, this Fossil Friday features the holotype of Fouquea superba, a winged insect of the order Palaeodictyoptera from the Upper Carboniferous of Commentry in France.
There have been three key innovations in the history of insects that contributed to the great success of this group. Those include the origin of wings and flight, the origin of foldable wings (Neoptera), and the origin of complete metamorphosis (Holometabola) (Nicholson et al. 2014). It is truly astonishing that all these three innovations appeared abruptly and very early among the oldest winged insects from the Carboniferous, which also exhibited a great diversity and disparity from the very beginning. I call this the Carboniferous Insect Explosion.
In the Pennsylvanian (Upper Carboniferous) subperiod between 323-299 million years ago, when the world was forming a single supercontinent Pangaea dominated by vast tropical swamp forests, this large diversity of different winged insect groups appeared suddenly without any known transitional forms in the older Mississippian (Lower Carboniferous) or Devonian strata (Strahler 1999, Labandeira 2005, Grimaldi & Engel 2005, Knecht et al. 2011, Nicholson et al. 2015, Wang et al. 2016, Bechly 2023a). According to leading experts, “an insect equivalent of an Archaeopteryx remains elusive” (Grimaldi & Engel 2005: 160).
The early fossil record of Carboniferous winged insects does not only include giant palaeopteran insects like the extinct palaeodictyopterids, mayflies, and dragonflies, or “primitive” neopteran insect orders like stoneflies, roaches, and orthopterans, but also thrips, bugs, and even advanced holometabolans like wasps, beetles, and scorpionflies, often with “a high degree of specialization early in the evolution of insects” (Garwood & Sutton 2010). Here is a brief and incomplete list of the large diversity of early winged insect groups in the Carboniferous with their oldest known representatives (also see Nel et al. 2013: fig. 3:
Palaeodictyopterids: Delitzschala (Germany, 323 mya)
Mayflies (Ephemeroptera): Triplosoba (France, 303-299 mya)
Dragonflies / Griffenflies (Odonatoptera): Eugeropteron and Geropteron (Argentina, 325-324 mya?)
Stoneflies (Plecoptera): Gulou (China, 318-314 mya)
Roaches (Dictyoptera): Kemperala (Germany, 318 mya) and Qilianiblatta (China, 318-314 mya)
Orthopterans: Archaeorthoptera (Czech Rep., 324 mya)
Thrips (Thysanoptera): Westphalothripides (France, 314-307 mya)
Plant lice (Psocodea): Westphalopsocus (France, 314-307 mya)
Bugs (Hemiptera): Protoprosbole (Belgium, 316 mya) and Aviorrhyncha (France, 314-307 mya)
Holometabolan larvae: Metabolarva (Germany, 314-307 or 306 mya) and Srokalarva (USA, 311-307 mya)
Wasps (Hymenoptera): Avioxyela (France, 314-307 mya)
Beetles (Coleoptera): Stephanastus (France, 303-299 mya)
Neuropteroids: Srokalarva (USA, 311-307 mya) seems to be a larval neuropteroid according to Haug et al. (2015)
Scorpionflies (Mecoptera): Westphalomerope (France, 318-314 mya)
Of course, there is always considerable uncertainty concerning the identification of such fossil insects. A good example is Adiphlebia lacoana from the Pennsylvanian Mazon Creek locality in Illinois. This taxon was identified as oldest beetle by Béthoux (2009), which was accepted by Wolfe et al. (2016) and even used as fossil calibration point for the dating of beetle origins. However, the attribution of Adiphlebia to beetles was disputed by Kukalova-Peck & Beutel (2012), who instead considered it as a stem neuropterid, while it was later identified as paoliid stem dictyopteran by Kirejtshuk et al. (2014). Rasnitysn & Aristov (2013) transferred Adiphlebia to the extinct family Anthracoptilidae, which was concurred by Guan et al. (2016), who thoroughly discussed the various hypotheses for the relationship of this family (i.e., Palaeodictyopteroida, Prothorthoptera, Hypoperlida, Eoblattida (= Cnemidolestodea), stem-Mantodea, Paraneoptera, Holometabola), but ultimately supported the newer alternative of a position in Paoliida as sister group of Dictyoptera. Even though the holotype specimen of Adiphlebia is a very complete and well-preserved fossil insect, it has been attributed in the past fifteen years by different experts to almost all of the major subgroups of winged insects. Keep this in mind when you read about the next discovery of a sensational transitional fossil in the news.
Where are the Stem Pterygotes?
Given that we find so many different subgroups of modern winged insects in the Carboniferous, shouldn’t we expect to find at least some stem-pterygotes among the earliest winged insects? What and where are they? Only two candidates were suggested, namely Palaeodictyopterida and Paoliida.
Palaeodictyopteroids are an extinct group of large insects with densely veined wings and sucking-piercing mouth parts. They rank among the oldest known winged insects and were considered to be stem-pterygotes by the godfather of paleoentomology Anton Handlirsch (1906-1908), but this is no longer believed among modern experts. Their phylogenetic position is still a matter of debate, but they are generally considered to be crown group pterygotes, either more closely related to living Palaeoptera (mayflies and dragonflies) or to living Neoptera (all other winged insects, with foldable wings) (Rasnitsyn & Quicke 2002, Grimaldi & Engel 2005, Prokop & Engel 2019, Prokop et al. 2019). Prokop et al. (2019) explicitly stated that “interestingly, Palaeodictyopterida have not been recovered as sister group to all other Pterygota.” In my view, their palaeopteran wing articulation, their wing venation, their genital organs with paired penes, and larval characters with abdominal winglet-like structures (Haug et al. 2014, Prokop et al. 2022, Ross 2022), all suggest a position of palaeodictyopteroids in Palaeoptera, most likely as sister group of modern mayflies.
Paoliida are another group of early pterygote insects from the Upper Carboniferous and Permian. Based on some obsolete earlier hypotheses (Sharov 1966, Rasnitysn 1976, also see Rasnitysn & Quicke 2002), Prokop et al. (2012) considered Paoliida as “putative stem-group of winged insects”, even though Prokop & Nel (2007) had already cautioned that such a view is not supported by any synapomorphies. Consequently, no other experts accepted this hypothesis. More recent studies (Prokop et al. 2014, 2023, Legendre et al. 2015) identified Paoliida as the sister-group of roachoids (Dictyoptera) within modern Neoptera, which was also accepted and endorsed by the previous supporters of the alternative stem-pterygote hypothesis.
The only remaining potential stem-pterygote could be Carbotriplurida, which was actually suggested in a study co-authored by myself (Staniczek et al. 2014) and accepted by some later studies (e.g., Prokop et al. 2023). However, Carbotriplura from the Upper Carboniferous of the Czech Republic is just a wingless insect similar to a giant silverfish, and its position in the basal stem group of winged insects is only based on speculative scenarios and slightly broadened paranota. It basically is a fossil that roughly fits a hypothetical model (also see Haug et al. 2014, Ross 2017, 2022, Prokop et al. 2022), but not a transitional fossil in any meaningful way. It did not have anything like real mobile wings and not even anything that would be clearly identifiable as gliding or parachuting airfoils. There is no evidence or proof that it was an arboreal animal capable of gliding, and its large size rather points against this hypothesis. But including a fancy evolutionary story increased the unique selling point and impact of our paper, which I can freely admit now that I am no longer part of the Darwinian establishment and no longer under pressure from any museum PR departments to oversell results in the international competition for grants and reputation.
Devonian Proto-Wing Insects Debunked
What about alleged Devonian proto-winged insects you might have read about in text books. Don’t they prove a gradual development of wings from wingless insects prior to the Carboniferous period? No they definitely don’t do anything like that, as all known examples (Eopterum, Rhyniognatha, and Strudiella) for such alleged transitional fossils have been debunked:
Eopterum devonicum and Eopteridium striatum were described by the famous Russian paleoentomologist Rohdendorf (1961, 1970) as the oldest fossil evidence of winged insects from the Devonian of Russia. The fossils indeed resembled isolated insect wings with the characteristic wing venation. This finding made it into textbooks for decades, and was even featured in Willi Hennig’s (1969, 1981) groundbreaking work on Insect Phylogeny with detailed interpretation and naming of the wing venation. However, shortly later Rohdendorf (1972) himself already suspected that the two fossil may rather represent nothing but the isolated tail fans (uropods) of a fossil shrimp, which was strongly confirmed by the American crustaceologist Frederick Schram (1980). Bummer!
Rhyniognatha hirsti is a fragment of an arthropod head capsule from the Lower Devonian Rhynie chert in Scotland, which is about 412 million years old. The common claim that it represents the oldest insect fossil and possibly a winged insect is based on a study by Engel & Grimaldi (2004). Some experts tentatively followed their interpretation, such as Edgecombe & Legg (2013), who said that “Rhyniognatha is known from a mandible that is certainly a member of the insect clade Dicondylia (i.e. having an anterior mandibular articulation) and may even be a pterygote (Engel and Grimaldi 2004). Rhyniognatha (Fig. 15.6) extends the range of winged insects downwards from the Carboniferous.” Based on its characteristic morphology, I had always thought that Rhyniognatha rather looks like the head of a myriapod. Some colleagues from the University of Tübingen and the Natural History Museum in Stuttgart, with whom I had discussed the issue over the years fully agreed. Lo and behold, a more recent and much more thorough study by Haug & Haug (2017) suggested that Rhyniognatha was misinterpreted and indeed represents an early centipede, which was also accepted by Ross (2022).
Finally, Garrouste et al. (2012) described yet another supposed fossil evidence for a winged insect from the Late Devonian of Belgium, which they called Strudiella devonica. An accompanying comment to the original description celebrated the discovery because “a complete insect fossil from the Devonian period has long been sought” and “the finding of a candidate may improve our patchy understanding of when winged insects evolved” (Shear 2012). Otherwise, the identification of this fossil was immediately met with scepticism, because it lacked any trace of wings or even nymphal wing buds (Taylor 2012). Indeed, the fame of this fossil did not last long, because a year later a team of other distinguished scientists found that Strudiella is just a decomposing crustacean (Hörnschemeyer et al. 2013). They could hardly have been clearer when they said that “we consider it to be crucial to prevent this fossil from entering entomology textbooks as an early insect.” The original authors of course still disagreed (Garrouste et al. 2013), but most paleoentomologists no longer believe in this oldest winged insect and consider the identity of this fossil as problematic due to its poor preservation (Haug & Haug 2017).
After the debunking of Strudiella, evolutionary biologists were left empty handed with no fossil record at all of any Devonian precursors for winged insects that were postulated to exist by molecular clock studies and of course were expected by Darwinian reasoning based on the fully developed winged insects in the Lower Carboniferous (see below). Nevertheless, Darwinian scientists made grandiose claims like the following by Engel et al. (2013), which are not supported by any valid fossil evidence:
Palaeological studies have advanced significantly in the last twenty five years,particularly with a large number of reevaluations of taxa in a cladistic framework and by pushing back the timing of wing origins from the early Carboniferous into the earliest Devonian perhaps latest Silesian.
Clueless about wing origins.
The identification of putative proto-winged insects is also hampered by the more general problem that we do not even know how proto-wings should have looked like, because the question of insect wing origins is far from settled in the scientific community (see Grimaldi & Engel 2005, Engel et al. 2013, Ross 2017, 2022, Smith & Jockusch 2020, Akst 2022, Prokop et al. 2022). There exist very different theories for their origin without any consensus: Fossil evidence rather supports the older paranotal theory of an origin of insect wings from stiff outgrowths of the dorsal breastplates (paranota) of the exoskeleton, while evo-devo data rather support the newer exite theory (Kukalová-Peck 1997) of an origin from mobile leg appendages (exites). Actually, different lines of data equally support both theories, which are seemingly incompatible and mutually exclusive. This conundrum led to the suggestion that both theories might be true and insect wings originated as composite structures from a fusion of stiff thoracic outgrowths with mobile leg appendages. This dual origin hypothesis was also suggested in a paper co-authored by myself (Staniczek et al. 2011), but in this mainstream paper I could of course not mention the elephant in the room: such a view would make viable intermediate forms hardly conceivable, so that a saltational adaptive macro-mutation (hopeful monster) would be required, which would arguably imply intelligent design. Even though several recent studies (mainly by the research team of Tomoyasu and Clark-Hachtel at Miami University; e.g., Clark-Hachtel & Tomoyasu 2020) increasingly supported the dual origin hypothesis, there are also new studies that still support one of the single-origin scenarios, such as the recent Nature papers by Bruce & Patel (2020), who suggested “that insect wings and body walls evolved from ancient leg segments,” or by Ohde et al. (2022), who suggested “the wing origin from lateral tergum of a wingless ancestor.” Another recent study by Fisher et al. (2021) suggests that the evo-devo data “doesn’t favor either of those hypotheses about wings,” but rather, “what it says is we need other kinds of evidence” (Jockusch in Akst 2022). In other words, we are pretty much as clueless about the origin of insect wings as a century ago
The Oldest Fossil Record of Winged Insects
So, since all the alleged Devonian proto-winged insects have been debunked, what are the oldest unambiguous winged insects found in the fossil record? They were all found in Namurian sediments near the border between the Lower Carboniferous (Mississippian) and the Upper Carboniferous (Pennsylvanian), such as the rich fossil insect fauna from the Hagen-Vorhalle quarry in Germany, but many cannot be precisely dated enough to count them as oldest record (Brauckmann & Brauckmann 1992, Brauckmann et al. 1994, Prokop & Hörnschemeyer 2016). But there exist two exceptions, which happen to represent both major subgroups of winged insects (viz Palaeoptera and Neoptera).
One prominent contender is Delitzschala bitterfeldensis, which belongs to the palaeodictopterid family Spilapteridae and has even preserved the characteristic banded color pattern of the wings. It was discovered in the drilling core of a well borehole from the Bitterfeld region in eastern Germany (Brauckmann & Schneider 1996), which has been dated to a uppermost Lower Carboniferous age (Lower Namurian A/E2, Arnsbergian) of about 323 million years. Until recently this represented the oldest well-dated fossil of a winged insect (see Ross 2017) and has therefore been used as calibration point for phylogenetic trees (Wolfe et al. 2016).
More recently, an unnamed insect has been discovered in the slightly older (lowermost Namurian A/E1, Pendleian) sediments from the Upper Silesian Basin in the Czech Republic (Prokop et al. 2005), which are about 324 million years old. Based on its wing venation it could be attributed to the polyneopteran order Archaeorthoptera
The Oldest Fossil Record of Metamorphosis
Actually, the first holometabolous insects with complete metamorphosis are recorded from the same Pennsylvanian subperiod (about 314-307 million years ago) as many of the other very early winged insects (Nel et al. 2013). Molecular clock data even suggest that Holometabola are at least as ancient (about 328-318 mya) as the earliest fossil record of winged insects at all (Labandeira 2011), or place “the origin of Holometabola in the Carboniferous (355 Ma), a date significantly older than previous paleontological and morphological phylogenetic reconstructions” (Wiegmann et al. 2009a, 2009b, Misof et al. 2014). My dear colleague and frequent co-author André Nel (2019) recently commented that “the late Carboniferous was also the time of the oldest known holometabolous insects, with complete metamorphosis (wasps, beetles, scorpionflies).” Indeed, as already listed above, fossils from larval and adult holometabolous insects of different orders have been found in late Carboniferous layers (see Kukalová-Peck 1997, Nel et al. 2007, 2013, Béthoux 2009, Kirejtshuk & Nel 2013, Kirejtshuk et al. 2014, Haug et al. 2015). The mentioned holometabolan groups all have a complete metamorphosis with a pupal stage, where the caterpillar-like body plan of the larval stage is dissolved into a kind of cell tissue soup and rearranged into the very different adult body plan of the winged imago. It is hardly possible to explain an evolutionary origin of this marvellous metamorphosis at all, as the only suggested hypothesis, the so-called pronymph-hypothesis by Truman & Riddiford (1999), has to make the extremely implausible assumption that the main feeding stage (caterpillar) originated from a non-feeding late embryonal stage (pronymph) (see Bechly 2023b). Apart from that, it is certainly unexpected to find this sophisticated ontogenetic process already with early flying insects rather than after hundreds of millions of years of gradual evolution
Clocks versus Rocks
Just like in most other groups of organisms we find a great mismatch between the estimated ages by molecular clock studies and the earliest fossil record, even though Darwinism would predict that these two different lines of evidence should converge to the same true history of life. Molecular clock studies dated the origin of winged insects at about 440-370 million years ago, but the oldest fossil record is just about 324 million years ago, which implies a ghost lineage of a whopping 116-46 million years. (Gaunt & Miles 2002, Regier et al. 2004, Rehm et al. 2011, Rota-Stabelli et al. 2013, Thomas et al. 2013, Wheat & Wahlberg 2013, Misof et al. 2014, Rainford et al. 2014, Tong et al. 2015, Wang et al. 2016, Johnson et al. 2018, Montagna et al. 2019, Schachat et al. 2023).
New Study Vindicates the Carboniferous Insect Explosion
Last year a new study (Schachat et al. 2023), which reviewed the fossil and molecular evidence for the age of winged insects, fully vindicated the explosive origin of winged insects in the Carboniferous. In their abstract the authors confirmed the stark conflict between molecular clock datings and the fossil record, which requires extensive ghost lineages of unrecorded history. They were not at all convinced by any previous explanations for this conundrum and concluded:
Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, … We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size.
Instead the authors suggested that the conflict between molecular clock and fossil record “is probably an analytical artifact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history [my emphasis].” Bursts in their early history is exactly what is described by me with the term Carboniferous Insect Explosion. I also agree that molecular clock datings are mostly rubbish, but this of course resonates better with intelligent design theory than Darwinian evolution, which would predict molecular clock studies to provide more accurate estimates on a regular basis.
The study also emphasized that different groups of insects appear in the fossil record roughly in the correct order as predicted by the sequence of branchings in phylogenetic reconstructions. Such cases of good stratigraphic fit indeed require an adequate explanation, which is arguably provided by common descent with modification. But the authors immediately qualified this result:
Obviously the fossil record is not sufficiently complete to expect that it recapitulates phylogeny with fine-tuned precision or accuracy, beyond the very broad-brush sequence of major taxa that are well represented as fossils; younger taxonomic units are expected to be less well represented as fossils, much less captured sequentially in the fossil record.
This suggests that the evidence for common descent from good stratigraphic fit may not be as strong as it is sometimes claimed.
Anyway, the abrupt appearance of winged insects with great diversity and disparity in the Carboniferous period, which we have called the Carboniferous Insect Explosion, is a phenomenon that is highly unexpected under Darwinian assumptions, but well be accommodated within an intelligent design paradigm. It represents just one of the many discontinuities in the history of life that strongly contradict the predictions from a neo-Darwinian theory of evolution. The same pattern is found in almost all groups of organisms, in all geographical regions, and in all periods of Earth’s history. This is clearly a signal in the data and not just noise. It is a signal that tells about a saltational history of life, with a series of bursts of biological creativity that can only be explained with the goal-directed infusion of new information from outside the system.
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Of mice ,men and the power of positive thinking.
Research with Mice May Explain How the Placebo Effect Works
The placebo effect is the best-known effect in medicine: We get better from an illness in part because we think we will. That’s not “just imagination”; it is proven by the best double-blind randomized clinical trials. When testing a new medication, researchers must subtract the placebo effect from their overall results in order to assess the medication’s true efficacy.
But how the placebo effect works in humans is something of a mystery. For example, it works even when patients know it’s a fake. And it may be getting stronger as researchers learn to manipulate it more effectively
Unexpected Results
A recent development from an experiment on mice sheds a bit of light. A group of researchers at the University of North Carolina, Chapel Hill, found circuits in the brain that unexpectedly play an role:
… researchers at the UNC School of Medicine — with colleagues from Stanford, the Howard Hughes Medical Institute and the Allen Institute for Brain Science — found a pain control pathway in the brain.
The researchers then showed that certain neurons and synapses along this pathway are highly activated when mice expect pain relief, with the mice experiencing pain relief even when no medication is involved.
MARK DEREWICZ, “BRAIN CIRCUITS OFFER PLACEBO EFFECT PAIN RELIEF,” UCCCH RESEARCH, JULY 31, 2024
How did the researchers know what the mice were expecting? As Adam Kovac explains at Gizmodo,
In their study, published this week in the journal Nature, the scientists trained mice by placing them in two connected chambers for a week. For the first few days, the floors of both chambers were pleasantly warm. Then, the floor of one chamber was made painfully hot, but the mice were able to seek shelter from the pain by scampering to the second chamber. Finally, on the last day, the floors of both chambers were made painfully hot. The mice, having been conditioned to expect relief upon reaching the second chamber, experienced some pain relief by virtue of the placebo effect. Upon reaching the second chamber, and despite it being just as hot as the first chamber, the mice displayed fewer behaviors associated with being hurt, such as jumping and paw licking.
ADAM KOVAC, “HOW PLACEBOS TRICK THE BRAIN INTO REDUCING PAIN,” GIZMODO, JULY 23, 2024
Not Nice to Mice
This sounds like cruelty to animals, yet something of value was learned. The mice had been injected with a virus that caused brain areas that experienced a change to light up. These were areas the researchers had not expected to be involved in pain control.
As they put it in their Abstract,
Here, we show that analgesia from the expectation of pain relief is mediated by rostral anterior cingulate cortex (rACC) neurons that project to the pontine nucleus (rACC→Pn), a pre-cerebellar nucleus with no established function in pain. We created a behavioral assay that generates placebo-like anticipatory pain relief in mice. In vivo calcium imaging of neural activity and electrophysiological recordings in brain slices showed that expectations of pain relief boost the activity of rACC→Pn neurons and potentiate neurotransmission in this pathway.
CHEN, C., NIEHAUS, J.K., DINC, F. ET AL. NEURAL CIRCUIT BASIS OF PLACEBO PAIN RELIEF.NATURE (2024). AN ACCELERATED PREVIEW OF THE PAPER IS OPEN ACCESS
Of course, with humans, things are likely to be more complex than with mice. The mice had to be placed in a very simple painful situation in order to trigger a placebo effect. With humans, it is often just a matter of communicating orally that “This [sugar pill] works!” But identifying new brain circuits that are changed by the expectation alone — the neural correlates of expectation — may help produce more effective pain control for both human and animals.
File under "well said" CX
"Descartes’ dictum: ‘There is nothing so absurd or incredible that it has not been asserted by one philosopher or another."
Paul Johnson
Thursday 8 August 2024
Darwinism is devolving?
Is This a Paradigm Shift?
My latest previous post, with David Klinghoffer, was about the “tipping point” in dissent from neo-Darwinism observed by Oxford physiologist Denis Noble, which he pin-pointed as occurring when the Royal Society convened in 2016 for the purpose of rethinking evolutionary theory. From Noble’s viewpoint, since 2016 defenders of neo-Darwinism have gotten very quiet, and young researchers in the emerging generation of scientists are happily working outside the framework of neo-Darwinism.
Not long ago at all, that sort of change seemed like a distant dream. As Douglas Axe put it in 2016, the academe had become a “self-righteous monoculture,” and I think Axe’s comment expressed how many people felt: “Maybe this regrettable situation will change, someday.”
“Maybe…someday.” Implied was: But don’t hold your breath.
The Zeitgeist is dead.
But that’s always how it feels when a certain climate of opinion is dominant and in line with the current zeitgeist. The dogma seems utterly unshakeable.
Until, one day, it doesn’t. C. S. Lewis (one of the most vehement critics of the zeitgeist qua zeitgeist) wrote
Nor can a man of my age ever forget how suddenly and completely the idealist philosophy of his youth fell. McTaggart, Green, Bosanquet, Bradley seemed enthroned forever; they went down as suddenly as the Bastille. And the interesting thing is that while I lived under that dynasty I felt various difficulties and objections which I never dared to express. They were so frightfully obvious that I felt sure they must be mere misunderstandings: the great men could not have made such very elementary mistakes as those which my objections implied. But very similar objections — though put, no doubt, far more cogently than I could have put them — were among the criticisms which finally prevailed.
An idea sits on its glorious throne. None dare question it. All its critics are doomed to perpetual quackdom. And then — just like that! — the zeitgeist changes. Suddenly, that “indisputable” idea is old-fashioned, out-of-date. People forget that they ever believed in it. Another philosophy takes its place, and it seems indisputable.
If Noble is right, that’s happening with neo-Darwinism. And it may be too much to hope, but there is some evidence the shift goes even beyond neo-Darwinism. Even Darwinism itself (without the “neo-”), maybe even the overarching philosophy of methodological naturalism, could be approaching a fall from power.
For example, Stephen Meyer perceives a shift in the public reception of intelligent design. In 2019, there was already a lot of interest in pro-ID content, but the responses tended to be very vicious. By 2023, the interest was still there, but the reactions seemed overwhelmingly positive. Meyer thinks this is a ripple effect from the deeper change that is underway, as arguments that have been percolating for decades begin to shift opinions in higher intellectual circles.
John West, meanwhile, has noted that opponents of intelligent design seem to be devolving in quality. Follow the downward trajectory from Darwin himself, to Stephen Jay Gould, to Richard Dawkins, to “loudmouth atheist” Jerry Coyne and P. Z. “hammer on the lunatics and idiots” Myers, to the likes of the YouTuber “Professor Dave” … The best of the best in the biology world just don’t seem that invested in attacking intelligent design or defending Darwinism anymore.
Meanwhile, in the broader philosophical scene, two of the New Atheist “four horsemen of the apocalypse” (Dawkins, Dennett, Hitchens, and Harris) have passed away, and no one seems queued to replace them. Ayaan Hirsi Ali, once a contender for fifth horseman (or first horsewoman?), has converted to Christianity. Dawkins himself recently commented that he doesn’t want to be remembered for being “vehement and an atheist.”
Something is changing.
...Long live the Zeitgeist!
But let’s not get too excited. Just because the paradigms are shifting does not mean that intelligent design is going to suddenly take the throne. There are other options. Panpsychism is on the rise. Vitalist theories are coming out of the shadows. Denis Noble’s methodologically naturalist Third Way group are trying hard to carve out a theory of biology that is independent of both neo-Darwinism and intelligent design, placing their hopes in various versions of teleonomy (internal teleology) and autopoiesis (self-construction) as explanations for biological complexity. Whatever emerges victorious from the milieu is likely to be neither intelligent design nor old-fashioned neo-Darwinism — just as whatever emerges from the larger philosophical debates will probably be neither crude materialism nor old-fashioned religious theism. There are other options there, too.
On that note: the lack of will among Dawkins and his sort to fight against ID may be mostly due to the fact that the shifting winds of culture have tossed many of the ID people and Darwinists (including Richard Dawkins and Jerry Coyne) onto the same side of some of the most heated debates. It’s not 2005 anymore, and the center of the “culture war” is no longer between the Religious Right and the New Atheists. Ayaan Hirsi Ali, for her part, has said that one reason she became a Christian was because “secular tools alone can’t equip us for civilizational war.”
Of course, not all proponents of intelligent design are religious, or politically on any particular side, or interested in civilizational wars. But atheist opponents of ID typically associate ID with religion, so if they find themselves on the same side as religious people in other ideological battles, they are naturally going to have less enthusiasm for attacking ID.
Get ready for...something.
It isn’t necessarily a positive development. While it’s encouraging that unquestionable tenets of Darwinism are now becoming questionable, and while there are some genuinely encouraging signs of a new openness to the theory intelligent design in many circles, it’s important to realize that the new zeitgeist will not necessarily be any better than the old one. If old enemies are forced to be friends, that could be because they’re having to deal with something worse than either of them.
For example, a power-driven post-truth paradigm could be worse than the old materialist paradigm. Stephen Meyer recently commented that he feels in a sense like a kindred spirit with Richard Dawkins, because both men care intensely about the big questions of life. I saw what Meyer meant when I watched Dawkins’s recent debate with the ex-atheist Ayaan Hirsi Ali. Dawkins brushed aside the critique that the ideas he promoted might have undermined Western civilization with the response that, essentially, that was none of his business: as a scientist, he cared about what was true, consequences be damned.
It sounded … old-fashioned. And that’s worrisome, because a post-truth paradigm is not likely to yield either truth or good pragmatic outcomes. If a post-truth attitude becomes entrenched in the new paradigm, we might look back nostalgically to the days when materialism was the main intellectual competitor.
At any rate we don't get a choice.
Whatever the new paradigm looks like, ID theorists are going to want to be at the cutting-edge of engaging with it. Right now, it may be tempting to treat panpsychism, self-construction, teleonomy, and whatever else comes up as frivolous distractions from the real intellectual opponent of Darwinism. But I think that would be a mistake.
As Denis Noble says, “neo-Darwinism is dead,” or at least dying. In the coming decades, the debate may be between, say, intelligent design and some sort of quantum physics-inflected marriage of scientism and spiritualism, not genuinely materialist, though haunted by the ghost of materialism. Because the coming victor is hard to see before it arrives, ID theorists need to be assessing new theories carefully as they emerge, not relegating them to mockery and dismissal. It would be a mistake to keep beating a dead horseman, and miss what’s coming up from behind.
Darwinism's supposed simple beginning is truly dead and buried?
“That Is a Lot of Evolution”: Study Finds LUCA Required 2,600 Genes
Recently I wrote about a study published in Nature Ecology & Evolution which found that the origin of life on Earth “required a surprisingly short interval of geologic time.” But I didn’t mention that the study reported the astounding complexity they inferred must have been present in that life — namely the Last Universal Common Ancestor (LUCA) of all living organisms. In short, they believe that LUCA must have had some 2,600 protein-coding genes — not that much different from many free-living bacteria or archaea that are around today. From the technical paper:
Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. … Altogether, our metabolic reconstructions suggest that LUCA was a relatively complex organism, similar to extant Archaea and Bacteria.
“A Fairly Large Genome”
Similarly, a write-up in Science expands on the meaning of the complexity:
The last ancestor shared by all living organisms was a microbe that lived 4.2 billion years ago, had a fairly large genome encoding some 2600 proteins, enjoyed a diet of hydrogen gas and carbon dioxide, and harbored a rudimentary immune system for fighting off viral invaders.
Likewise a commentary in Nature Ecology & Evolution states
Our results indicate that the LUCA existed between 4.09 and 4.33 billion years ago, a few hundred million years after the moon-forming impact. Our reconstruction of the genome of the LUCA is over 2.5 megabases, comparable to living bacteria, and encompasses at least 2,500 protein-coding genes. The LUCA was capable of nucleotide and protein synthesis, possessed a cellular envelope, and used ATP as an energy currency. … We also found that the LUCA possessed an RNA-based immune system … LUCA must have been part of a broader ecosystem, of which it represents the only living descendant.
Although some aspects of our study are in good agreement with previous work on the LUCA, we infer a larger genome size and genetic repertoire than most previous studies.
This means that not only did life emerge rapidly, but life with a genome composed of thousands of genes and with millions of base pairs emerged rapidly. This is astounding.
Evolutionary Reasoning at Work
Now we must understand that their inferences about LUCA are all based upon evolutionary reasoning. LUCA of course is a hypothetical evolutionary postulate. As such, it depends on universal common ancestry being true. I’m a skeptic of universal common ancestry for various scientific reasons. However, once you understand the reasoning they use to infer the complexity of LUCA, you appreciate the conundrum that this kind of a study poses for naturalistic accounts of the origin of life. An article in the Washington Post invites readers to “Meet the surprisingly complex ancestor of all life on Earth.” It explains the methods that were used:
The new timeline and details can be chalked up to more advanced analysis methods available today. In the new study, the team of 19 scientists used a combination of genetic analysis and fossil records to determine the age of LUCA and its characteristics. They first compared genes in modern genomes of bacteria and archaea to determine which gene families were present in LUCA. They estimated LUCA’s genome size, the number of proteins it encoded and its metabolism.
In other words, by comparing the genomes of modern organisms, they were able to infer the minimal sets of genes that must have been present if in fact they are all descended from a common ancestor. The bottom line? It’s a lot of genes — making LUCA more complex than many evolutionary theorists probably expected to find. As the Washington Post noted:
In the most extensive analysis of the organism to date, scientists propose in a new study that this hypothesized ancestor was more sophisticated than previously known — thought to possess an immune system to fight off viruses, for instance.
The team said LUCA appeared around 4.2 billion years ago, shortly after Earth was thought to be habitable, suggesting it evolved even quicker than previous estimates and survived through tumultuous times on the planet.
[…]But LUCA may have been more complex than they previously thought, the authors found. They inferred it had an immune system that fought viruses and found evidence suggesting it contained genes to protect against ultraviolet damage and lived at the ocean surface.
The lead author of the study was quoted as saying, “[T]his was a fairly complex organism, already possibly by the time of like 4.2 billion years ago.” Another scientist commented, “LUCA was a very complex cell, with a genome similar to modern bacteria (which we think of as simple, but from a molecular biology perspective are very complex).”
That latter scientist was further quoted saying: “That is a lot of evolution to happen within 100 million years or less.” A lot of evolution, indeed.
An Unanswered Question
This leaves unaddressed the question of whether organismal life, a “very complex cell,” could exist at all below the threshold of complexity that the study attributes to LUCA — without, for example, sophisticated defenses such as an “immune system that fought viruses” or “genes to protect against ultraviolet damage.”
Would a much simpler cell be viable? To think so pushes the envelope of plausibility. If it would be viable, someone needs to explain how such a defenseless life could survive to reproduce. If it wouldn’t, the strong suggestion is of life springing from non-life without a far simpler yet viable transitional state.
Transitions like that, including very rapid ones, are a hallmark of human-devised technology. In the context of the early Earth, it sounds like the act of a creative agent, existing before the first cell came to be. In other words, it sounds like intelligent design.
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