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Saturday, 7 January 2023
The question of the millennium: Can we talk about this?
Copernicus redux?
paper demonstrates superiority of the design heuristic
Friday, 6 January 2023
A heavenly witness against design deniers?
Animals Tune Behavior by Lunar Cycle; but How?
David Coppedge
Tonight’s moon will be full, so here is a timely question. Many unrelated animals tune their behavior by the lunar cycle. How do they do it, given that sunlight overpowers moonlight?
Researchers in Austria think they have found a clue: a cryptochrome protein that appears to respond to the lunar cycle. Cryptochrome proteins are also implicated in the geomagnetic sense in birds. Whatever they found, it surely must represent only a piece of a biological puzzle. Let them explain in this from the University of Wien:
Many marine organisms, including brown algae, fish, corals, turtles and bristle worms, synchronize their behavior and reproduction with the lunar cycle. For some species, such as the bristle worm Platynereiis dumerilii, lab experiments have shown that moonlight exerts its timing function by entraining an inner monthly calendar, also called circalunar clock. Under these laboratory conditions, mimicking the duration of the full moon is sufficient to entrain these circalunar clocks. However, in natural habitats light conditions can vary considerably. Even the regular interplay of sun- and moon creates highly complex patterns. Organisms using the lunar light for their timing thus need to discriminate between specific moon phases and between sun and moonlight. This ability is not well understood.
The first statement should alarm evolutionists. Circalunar clocks are found in very unrelated animals (evolutionarily speaking): vertebrates like fish and turtles and invertebrates like worms and corals. Each of these must have hit upon lunar tuning independently.
The researcher’s paper in Nature Communications points out that we humans have connections to the lunar cycle, too:
In addition, lunar timing effects have also been documented outside the marine environment, and recently uncovered correlations of human sleep and menstrual cycle properties with moon phases have re-initiated the discussion of an impact of the moon even on human biology. As recently documented for corals, desynchronization of these reproductively critical rhythms by anthropogenic impacts poses a threat to species survival.
The Bristle Worm as a Test Case
Unbeknownst to most landlubbers, polychaetes rule the seas. There are at least 10,000 species of these swimming bristly worms, some of which pop with brilliant colors or light up with a bioluminescent glow. They’ve adapted to every imaginable marine habitat, from deep hydrothermal vents to crowded coral reefs to the open ocean—and many have found ways to survive that are definitely bizarre.
Interested readers can browse through Smithsonian’s list of facts and look at the pictures. A short horror movie shows a lionfish learning too late not to mess with a bobbit worm (Eunice aphroditois), a different species of bristle worm in the Atlantic. It’s a creature of nightmares, so be forewarned. The poisonous lionfish can’t use its defensive weapons against this lightning-fast monster: a worm! It’s a terrifying creature right out of the movie Tremors. More about bobbit worms can be found at ARCReef.com. Do not read this: some bobbit worms grow up to ten feet long! Fortunately, attacks on humans are rare, limited to “nasty bites” (Daily Mail).
Evolutionary Challenges
Back to P. dumerilii, a much more benign polychaete only 2-4 cm long. A type of ragworm, this species is found worldwide. Wikipedia calls it a living fossil. Although it’s an invertebrate, “it has an axochord, a paired longitudinal muscle that displays striking similarities to the notochord regarding position, developmental origin, and expression profile.” It swims with a coordinated system of cilia on its surface. “Whole-body coordination of ciliary locomotion is performed by a ‘stop-and-go pacemaker system’,” the article says. That’s not the only pacemaker in this amazing little worm. Despite having “a pair of the simplest eyes in the animal kingdom,” it can “see” the phases of the moon. Those little eyes do not help the evolutionary story:
The ciliary photoreceptor cells are located in the deep brain of the larva. They are not shaded by pigment and thus perceive non-directional light. The ciliary photoreceptor cells resemble molecularly and morphologically the rods and cones of the human eye. Additional [sic], they express an ciliary opsin that is more similar to the visual ciliary opsins of vertebrate rods and cones than to the visual rhabdomeric opsins of invertebrates.
The bristle worm’s genome also challenges Darwinism:
The genome of Platynereis dumerilii … contains approximately 1 Gbp (giga base pairs) or 109 base pairs. This genome size is close to the average observed for other animals. However, compared to many classical invertebrate molecular model organisms, this genome size is rather large and therefore it is a challenge to identify gene regulatory elements that can be far away from the corresponding promoter. But it is intron rich unlike those of Drosophila melanogaster and Caenorhabditis elegans and thus closer to vertebrate genomes including the human genome.
Wikipedia prudently abstains from speculating on how these worms evolved.
Possible Lunar Oscillator Found in P. dumerilii
In the introduction to the paper, the authors say, “Despite the importance and widespread occurrence of lunar rhythms, functional mechanistic insight is lacking.” They found a cryptochome protein they call L-Cry that appears to keep time to the full moon. Its asymmetric dimer appears to have two monomers with very different light sensitivities, which “provides the molecular basis to sense and interpret light intensities across five orders of magnitude.”
This is important because full sunlight swamps moonlight, so the worm brain must be able to discriminate the smaller peaks of illumination from larger ones. Additionally, L-Cry must be able to avoid being tricked by artificial light that can also outshine full moonlight. It must also be robust against darkness on cloudy full-moon nights and by “natural acute light disturbances, such as lightning.”
Experiments in the “worm room” under controlled simulations of sun and moon illumination cycles demonstrated this ability. “L-Cry’s major role could be that of a gatekeeper controlling which ambient light is interpreted as full-moonlight stimulus for circalunar clock entrainment,” they say. If an organism can set its lunar clock to a full moon, it can also discriminate other lunar phases.
The full moon is unique in having the longest duration of light at night, followed by sunrise. A circalunar clock presupposes, therefore, the ability to measure the duration as well as intensity of light. L-Cry may do this with a ratchet mechanism: as the protein accumulates photons, it reaches higher quantum levels that photoreduce parts of the low-sensitivity monomer. The authors also observed L-Cry accumulating in the nucleus and diminishing in the cytoplasm during the simulated moonlight exposure time. “This suggests that different cellular compartments convey the different light messages to different downstream pathways.”
Even so, this cryptochrome discovery only delivers “the first molecular entry point into the mechanisms underlying a moonlight-entrained monthly oscillator.” The photoreceptor for L-Cry is unknown. Additionally, L-Cry must cooperate with the circadian clock genes, adding to the regulatory complexity. How these proteins signal a cascade of physiological behaviors when it’s time to spawn remains curious. “Certainly, more extensive mechanistic studies are required to further verify our models.”
Convergent Functionality
Finally, an evolutionary consideration: Monthly synchronization by the moon has been documented for a wide range of organisms– including brown and green algae, corals, crustaceans, worms, but also vertebrates… Furthermore, recent reports also provide increasing evidence that the lunar cycle influences human behavior… Are the lunar effects mediated by conserved or different mechanisms?
Since L-Cry is not known in these other species, the authors speculate that either conservation of other proteins will be discovered, or that other proteins with analogous functions will be found.
Last, but not least the molecular mechanisms underlying the circalunar oscillator also await identification, and it is possible that conservation exists on this level. Examples are known from circadian biology and it will now require further work to reach a similar level of understanding for moon-controlled monthly rhythms and clocks.
Surely, though, conservation of function using entirely different molecular mechanisms poses a severe challenge to Darwinism. It would seem to require entirely different sets of mutations to be selected for a common function. In design theory, intelligence starts with the concept and can use different instruments to play the same tune.
The Palolo Worm
We end with a spectacular case of circalunar time tuning. Another polychaete, the Palolo Worm of the South Pacific, undergoes a remarkable reproductive cycle timed to both lunar and annual cycles. Britannica explains its life cycle:
The palolo worm of the South Pacific (Palolo siciliensis [P. viridis or Eunice viridis]) inhabits crevices and cavities in coral reefs. As the breeding season approaches, the tail end of the body undergoes a radical change.The muscles and most of the organs degenerate, and the reproductive organs rapidly increase in size. The limbs on the posterior segment become more paddlelike. After the animal backs part way out of its tubelike burrow, the posterior section breaks free and swims to the surface as a separate animal, complete with eyes. The anterior end, still attached to its tube, regenerates a new posterior end.
The free-swimming half-worms contains sperm and eggs. Tens of thousands of these half-worms swim to the surface as if on cue, and release their reproductive cells always at the same time of year and at a particular phase of the moon.
The free-swimming section always makes its appearance in the early morning for two days during the last quarter of the Moon in October. Twenty-eight days later, it appears in even greater numbers in the final quarter of the November Moon. At the surface of the sea the sperm and eggs are discharged, and fertilization occurs. Palolo tails, considered a delicacy by the Polynesians, are gathered in vast numbers during swarming.
Worms. Such simple, lowly creatures. But what wonders await the biologists who delve into their mechanisms. Like everything else in biology, design-inspired awe explodes in the details.
The fossil record continues to be a bomb thrower for Darwinism
Fossil Friday: Fossil Golden Moles and the Abrupt Origin of Afrosoricida
Günter Bechly
Last week we looked into the fossil history of elephant shrews. This first Fossil Friday in the new year we will move on in our series on placental mammal origins to another group of mainly insectivorous afrotherians: the order Afrosoricida, which comprises golden moles (Chrysochloridae), otter shrews (Potamogalidae), and the iconic tenrecs (Tenrecidae) from Madagascar. As in other small mammals their fossil record mostly consists of isolated jaw fragments and teeth, just like the featured fossil of the golden mole Diamantochloris inconsessus from the Eocene of Namibia (Pickford 2018).
Mainly based on molecular data (Springer et al. 2003) it has been suggested that the Afrosoricida originated 65 million years ago, right after the K/Pg impact event or even before (Tabuce et al. 2007: fig. 5, Poux et al. 2008: fig. 3, Everson et al. 2016: fig. 4). Of course, the fossil record does not at all support such a view (Sargis & Dagosto 2008: fig. 5.17, Asher 2010: fig. 9.1), so that some authors decided within a year to simply place the assumed origin 10 million years later (Tabuce et al. 2008: fig. 1). Isn’t evolutionary biology a wonderful science? Here is a brief list of the oldest known fossil genera in each group of Afrosoricida with their estimated stratigraphic range (based on PaleoDB and Seiffert 2010):
Afrosoricida (48.60–0 mya)
Chrysochloridae (48.6–0 mya)
Damarachloris Pickford, 2019b (48.6–40.4 mya)
Diamantochloris Pickford, 2015a (48.6–40.4 mya, primitive Chrysochloridae acc. to Pickford 2018)
Namachloris Pickford, 2015c (40.4–37.2 mya)
Prochrysochloris Butler & Hopwood, 1957 (20.43–15.97 mya)
Tenrecoidea (= Tenrecomorpha) (48.6–0 mya)
Dilambdogale Seiffert, 2010 (37.2–33.9 mya, rather about 37)
Eochrysochloris Seiffert et al. 2007 (33.9–28.4 mya, rather about 33)
Jawharia Seiffert et al. 2007 (33.9–28.4 mya, rather about 33)
Nanogale Pickford, 2019a (48.6-40.4 mya)
Plesiorycteropus Filhol, 1895 (0.012–0.0 mya)
Qatranilestes Seiffert, 2010 (33.9–28.4 mya, rather about 30)
Widanelfarasia Seiffert & Simons, 2000 (33.9–28.4 mya, rather 33.9)
Potamogalidae (40.4–0 mya)
Namagale Pickford, 2015b (40.4–37.2 mya)
Tenrecidae (40.4–0 mya)
Arenagale Pickford, 2015b (40.4–37.2 mya)
Erythrozootes Butler & Hopwood, 1957 (24-16 mya)
Parageogale Butler, 1984 (= Butleriella) (24-16 mya)
Protenrec Butler & Hopwood, 1957 (23.03–11.608 mya)
Sperrgale Pickford, 2015b (40.4–37.2 mya)
Golden Moles (Chrysochloridae)
Golden moles are small, burrowing mammals endemic to sub-Saharan Africa with 21 living species (Asher et al. 2010). The oldest and most primitive fossil golden moles, Diamantochloris and Damarachloris, were discovered in Middle Eocene (Lutetian) sediments from Black Crow in Namibia, which are maximally 48.6 million years old (Pickford 2015a, 2018, 2019b). Together with the tenrecomorph Nanogale (see below) they also represent the earliest fossil record of Afrosoricida known so far. The best known but slightly younger genus is Namachloris, of which about 120 remains from almost the complete skeleton have been found (Pickford 2015c). They show that even these early representatives already had the burrowing adaptations of their living descendants. Another very old alleged chrysochlorid is Eochrysochloris from Fayum in Egypt (Seiffert et al. 2007, Seiffert 2010). However, Pickford (2015a, 2015c, 2018) suggested that Eochrysochloris “is probably not a chysrochlorid” but rather a tenrecid.
Tenrecoidea
The oldest representative of Tenrecoidea or Tenrecomorpha is Nanogale fragilis from the Eocene freshwater limestone of Black Crow in Namibia that can be dated to maximally 48.6 million years (Pickford 2019a). There is only a single mandible fragment known, which represents the smallest mammal from the fossil record in Africa. It has some characteristics resembling tenrecs and others rather resembling otter shrews, so that it may belong to their common ancestral lineage. Other very old tenrecoids were found in Eocene/Oligocene (37-30 mya) outcrops of the Jebel Qatrani Formation in the Fayum region of northern Egypt (Seiffert 2006), and include the genera Dilambdogale, Eochrysochloris, Jawharia, Widanelfarasia, and Qatranilestes (Seiffert & Simons 2000, Seiffert et al. 2007, Seiffert 2010).
Otter Shrews
Otter shrews (Potamogalidae) only include two living genera with three species of nocturnal and amphibious mammals, feeding off crustaceans and fish. They are believed to be closely related to the Malagasy tenrecs but only occur in Western and Central Africa. According to molecular clock studies their lineage should at least date to the Lower Eocene (Everson et al. 2016), but the possible fossil record is very sparse and controversial. Van Valen (1967) thought that the genera Erythrozootes and Protenrec might be fossil otter shrews, but most other and later workers rather attributed them to the genuine tenrecs. Seiffert (2007) again found the Miocene Protenrec as sister group of Potamogale instead on tenrecs, but subsequent studies did not accept this position. The only unequivocal fossil record of otter shrews is Namagale described by Pickford (2015b) from the Late Eocene (Bartonian) Eocliff in Namibia, which is 40.4-37.3 million years old.
Tenrecs
Living tenrecs are hedgehog-like mammals endemic to Madagascar with 31 living species classified in 8 genera and 3 subfamilies. Until recently the oldest fossil tenrecs were the three genera Erythrozootes, Parageogale, and Protenrec from the Miocene of Kenya and Namibia (Butler & Hopwood 1957, Butler 1984, Poduschka & Poduschka 1985, McKenna & Bell 1997, Mein & Pickford 2003, 2008, Asher & Hofreiter 2006, Seiffert et al. 2007, Pickford et al. 2008, Poux et al. 2008, Asher & Seiffert 2010). Strangely, these genera seem to be most closely related to the Malagasy tenrec genus Geogale (Asher & Hofreiter 2006). Poduschka & Poduschka (1985) disputed the relationship of Parageogale, which they had invalidly named Butleriella, with the living genus Geogale, but this very relationship was vindicated by new material and further studies (see Asher & Seiffert 2010). This relationship arguably would imply a back dispersal event from Madagascar to Eastern Africa more than 267 miles across the Mozambique Channel of the Indian Ocean (Douady et al. 2002, Poux et al. 2008, Everson et al. 2016). This is a quite daring hypothesis to say the least (see Bechly 2018). Apart from this anomaly the general colonization of Madagascar by tenrecs has been dated with molecular evidence to have happened between 55 mya and 37 mya by Douady et al. (2002) or between 56-30 mya by Everson et al. (2016), which falls well within the range of the oldest African fossil stem tenrecs and well after the separation of Madagascar from mainland Africa about 165-120 mya.
These oldest putative stem tenrecs are the two species Arenagale calcareus and Sperrgale minutus described by Pickford (2015b) from the Late Eocene (Bartonian) Eocliff in Namibia, dated to about 40 million years ago.
We should also briefly mention the Malagasy Aardvark Plesiorycteropus, which is known from two subfossil species. Apparently, these animals went extinct just a few hundred years ago, likely due to anthropogenic causes like overhunting and deforestation. They were long believed to be related to Xenarthra or Tubulidentata, and even assigned to its own distinct mammal order Bibymalagasia. However, a molecular study of ancient collagen revealed that they represent another major branch of Tenrecoidea (Buckley 2013), though no older fossils are known yet.
But, we have not yet exhausted the potential candidates for the oldest Afrosoricida. There are two obscure fossil mammals from the Late Paleocene of Morocco that may qualify: Todralestes variabilis was originally described as an insectivoran of the polyphyletic waste basket taxon “Proteutheria” (Gheerbrant 1991, 1994, Gheerbrant et al. 1998), while Afrodon chleuhi was described from the same outcrops as an insectivoran of the extinct family Adapisoriculidae (Gheerbrant 1988, Gheerbrant & Russell 1989, Gheerbrant et al. 1998).
Both Todralestes and Afrodon share dental similarities with supposed early afrosoricids like Widanelfarasia, Protenrec, and Dilambdogale (Seiffert & Simons 2000, Seiffert et al. 2007). Asher & Seiffert (2010) and Seiffert (2010) even recovered these two genera as most basal stem Afrosoricida in their cladogram. If this should be correct, it would place the origin of the afrosoricid lineage into the Late Paleocene, right in the brief window of time when most of the placental mammal orders first appear in the fossil record. Of course, as always there is considerable disagreement about the phylogenetic affinities of these taxa: Tabuce et al. (2008: fig. 1) put a question mark at the alleged Late Paleocene occurrence of stem afrosoricids suggested by Seiffert et al. (2007), without explicitly listing the concerning genera. Pickford et al. (2008) considered Todralestes as a member of the unrelated extinct mammal order Cimolesta, and Afrodon still as an adapisoriculid insectivoran of the living mammal order Lipotyphla. The consensus tree of Halliday et al. (2015) did neither support a relationship of Todralestes nor of Widanelfarasia and Dilambdogale with Afrosoricida or even Afrotheria.
Like in all the other groups of afrotherian mammals, the modern consensus of attributing Afrosoricida to the African mammal clade Afrotheria is almost exclusively based on molecular data (Nishihara et al. 2005, Seiffert 2003, 2007, Tabuce et al. 2007, 2008, Asher & Seiffert 2010, Heritage et al. 2020), while anatomical similarities were universally interpreted as evidence for a relationship with insectivorans (e.g., Van Valen 1967, Butler 1984, Novacek et al. 1985, McKenna & Bell 1997) and even explicitly rejected an afrotherian clade (Asher 1999). Pickford (2019a) mentioned that “many recent phylogenetic analyses of Afrotheria seem to be incompatible with each other.”
A Repeating Pattern
Again and again we find the same pattern:
Darwinism predicts gradual accumulation of small changes over long periods of time but the empirical data of the fossil record point to rapid bursts of biological novelty.
Darwinism predicts that anatomical similarities should align with genetic similarities but the actual trees and/or classifications generated from these data conflict with each other.
Darwinism predicts that molecular clock estimates should agree with the stratigraphic appearance of taxa in the fossil record but they don’t.
Should we draw any conclusions from such consistent empirical failures of a theory? Maybe we should instead modify a popular dictum by the famous evolutionary biologist Theodosius Dobzhansky into “Nothing makes sense in biology in the light of (Darwinian) evolution” to align it better with reality.
Next Fossil Friday we will have a look at the early fossil record of hyraxes, another afrotherian group with an interesting history.
A hill to die on?
Astrophysicist Bijan Nemati: Why Intelligent Design Matters
Evolution news
Thursday, 5 January 2023
Darwinism's simple beginning problem 2.0?
Minimal Complexity Problem in Prey Detection by the Sand Scorpion
A Spectacular Ability
Irreducible Complexity
Tito: a brief history.
Josip Broz Tito
Wikepedia
Ann Guager on becoming Ann Guager
The Evolution of Dr. Ann Gauger
Stephen Dilley
Editor’s note: We are delighted to present a new, occasional series on the “evolution” of top scientists who have helped advance the case for intelligent design.
“It was like the cast of characters from an Illustra Media film.”
That was biologist Ann Gauger’s droll comment on her first visit to Discovery Institute’s offices in Seattle. The year was 2004. Dr. Gauger’s scientific credentials had caught the eye of Stephen Meyer and he had invited her to come talk with him. On the day of the meeting, Gauger arrived and settled into a conference room. In walked Meyer, Jay Richards, and Jonathan Wells — the usual suspects from Illustra films such as Unlocking the Mystery of Life.
The occasion of the meeting went back to two weeks earlier. A friend had recommended to Gauger an article in DI’s newsletter, Nota Bene. The article summarized Steve Meyer’s controversial piece on the Cambrian explosion in the peer-reviewed journal Proceedings of the Biological Society of Washington.1
Gauger had been reading ID literature for some time. She was interested and decided to subscribe to Nota Bene. When she signed up, she included “PhD” after her name. “I wonder what will happen?” she mused.
Twenty minutes later, she received a phone call from Logan Gage, an administrative liaison. Logan went through a checklist.
“You have a PhD, right?”
“Yes.”
“You’re aware of the Dissent from Darwin list?”
“Yes. In fact, I’ve already signed it.”
A pregnant silence. Then a reply, “Can you send me your CV?”
Gauger promptly did so. “I wonder what will happen?” she thought again.
Twenty minutes later, Logan was on the phone again. “Can you come in to DI to talk with Steve Meyer?” Nothing was the same after that.
Evolution as Default
Yet by the time Gauger watched the Illustra movie cast walk into the room at Discovery Institute in 2004, her concerns about evolution had grown. Why? There were many reasons, yet chief among them was the Cambrian explosion.
The fossils of the Cambrian era raised the puzzle that Gauger had pondered while studying invertebrates: how did all of these different body plans emerge? Of the 27 phyla recorded in the fossil record, an astonishing 20 of them emerged during the Cambrian explosion. Only 3 phyla appear before the Cambrian, and only 4 others appear after that era.2 It is the major event within organic history.
Gauger also realized that the neo-Darwinian mechanism lacked the creative power to generate so many new body plans in the time available.3 And even the promise of evo-devo had fallen short. In particular, Gauger was impressed with the Nobel Prize-winning work of Christiane Nüsslein-Volhard and Eric Wieschaus. These geneticists had studied the fruit fly Drosophila melanogaster, mapping its genome and analyzing is early development. They discovered that mutating or perturbing early-acting body plan molecules invariably kills the fruit fly.4 In order to generate a genuinely new body plan, early embryonic changes must take place. Yet for evolution to occur, these changes must be viable rather than lethal. By contrast, Nüsslein-Volhard and Wieschaus observed that early developmental mutants never even hatched as larvae.5 Other problems plagued evo-devo, too.6
Moreover, Gauger’s own research after 2004 helped illuminate key problems for evolutionary theory. Among others, she articulated the causal circularity problem,7 the waiting times problem,8 and the implausibility of human evolution.9 Gauger has also helped to show that a first couple is possible in the context of human origins.10 And more on the way: a volume she has edited on the positive case for intelligent design, by contributors arguing from a Catholic perspective, is just around the corner.11
Full Circle
Gauger recalls with a chuckle her initial meeting with the Illustra cast in 2004. “Steve Meyer walked me through his PowerPoint presentation on the Cambrian explosion. He had the right argument. But I spotted a typo and said so.”
The “typo,” as it turns out, was a technical point about invertebrates. Only someone well-versed in the field would have had that kind of knowledge. Dr. Gauger’s years of research and study had prepared her perfectly for the road ahead.12
Evolution by design v. Design by Evolution?
Brain Scientist: Consciousness Didn’t Evolve; It Creates Evolution
Denyse o' Leary
In a recent episode of Closer to Truth, Robert Lawrence Kuhn interviewed University of California cognitive scientist Donald Hoffman on a challenging topic, “Why did consciousness emerge?”:
There was a time when there was no consciousness in our universe. Now there is. What caused consciousness to emerge? Did consciousness develop in the same way that, say, the liver or the eye developed, by random mutation and fitness selection during evolution? Inner experience seems to be radically different from anything else. Are we fooling ourselves?
Donald Hoffman is the author of Visual Intelligence: How We Create What We See and coauthor of Observer Mechanics: A Formal Theory Of Perception (Norton, 2000).
A partial transcript and some notes and questions follow:
Robert Lawrence Kuhn: Don, you make the extraordinary claim, backed up by some sophisticated computer simulations that evolution, by favoring fitness, drives truth to extinction. Yeah, how then can we deal with reality and what are the implications of that? (0:19)
Donald Hoffman: It’s such an extraordinary result. It is at first a little bit surprising and you would wonder how could true perceptions be useful? How could it possibly be that true perceptions could guide useful behavior? And fortunately we have a nice metaphor with the advent of computers and laptops and user interfaces that I think can help us to see what’s going on here. (0.41)
If you look at your laptop interface … you might have a blue rectangular icon for a file that you’re working with and that icon might be in the lower right hand corner of your of your screen. Does that mean that the file itself, that you’re working on, is blue or rectangular or in the lower right hand corner of the computer? Well, obviously not. (1.06)…
The whole point of the desktop interface is to hide the truth and to guide your behavior. You don’t want to know about the diodes and the resistors and all the electronics inside there and all the magnetic fields and voltages and all the software. If you had to know all of that stuff you could never paint a picture, you know, edit your photograph or write a paper. So what you want is an interface that hides the complexity that you don’t need to know so that you can do the things you need to do. (2:02)… It’s not lying to you; it’s actually helping you. But it’s helping you by hiding the truth. (2:16)
So evolution has done the same thing for us. It has given us perceptions that are like a user interface (3:06)…
Note: Let’s leave “evolution” out of this for a moment. Here is what we know, irrespective of how we came to know it: All sources of information, however derived, are specific and partial. Through an open window, I see a herd of deer trotting across the parking lot. A sharp-eared neighbor, not near the window, hears their hooves striking the pavement. A small dog in a pen under the window senses the deer by their smell and may even guess their size and sex in some cases. Not one of us sees the whole picture. In the same way, humans, using abstractions, develop symbol systems on computers to represent functions. All information systems necessarily represent information filtered in some way. But — absent any reason to believe that the information provided is erroneous — what does that prove about truth or consciousness? Kuhn picks up on one aspect of this:
Robert Lawrence Kuhn: Now is your metaphor a strong metaphor or have you thought deeply about it? Because that metaphor is enormously powerful in terms of reflecting our lack of capacity of understanding what reality is. I mean, it would be hopeless, it’s impossible to tell from the user interface on a computer, just what the source code is. But all the electronics and the voltages and the capacity and the structure of the CPU… I mean that’s just so far beyond anything that you would even know existed (3:29)
Donald Hoffman: I agree. I mean if someone were to say, I want you to use only what you see on the desktop the pixels and tell me what’s going on and from that figure out a theory about what’s going on inside the computer that’s going to be a really, really tough time… (4:00)
Note: But we don’t need to know everything about how a computer works to use the desktop icons to get us where we need to go, any more than observers need to know much about deer in order to determine whether they are present. Again, all information is necessarily partial and focused and our consciousness enables us to determine the information that we need. To get more information, we formulate a specific question, to which the answer will likewise be partial and focused. To see everything as a whole we would need an unlimited consciousness. That is what many people call God.
Donald Hoffman: Right. So you have to make assumptions, right? So you’re free to make assumptions and I’ll just jump to the assumption I make here to solve the problem. So I don’t take our perceptions of space and time as literally true. I take them as a desktop. (4:19)
To solve the mind–body problem I’ve tried to say, let’s take consciousness as fundamental. So what’s behind the interface is consciousness, right, just like in the example of the computer. what’s behind the screen are all those diodes and resistors and so forth. Yeah, I’m saying what’s behind space and time and physical objects for us is a world of what I call conscious agents or consciousness. (4:41)
The nice thing about that theory is, I’m conscious, you’re conscious. I’m proposing that the objective reality behind this interface is not utterly alien to who I am. There is a chance for me to begin to understand that objective reality behind the interface because I’m not utterly separated from it so it’s a different situation than what’s behind the computer screen so anyway. (5:07)
But what happens when you then ask the, question where your consciousness came from?, because it came through an evolutionary process right? So, when you take this point of view now, if space and time were not fundamental, right, then we have to rethink evolution from the get-go. (5:26)
Note: At this point, we surely do need to rethink evolution from the get-go. Hoffman sounds like an philosophical idealist. He calls his position conscious realism. But according to current evolution theory, consciousness is a randomly evolved illusion created by the brain to help the human animal hunt better. To grant any primacy to consciousness is to imply that the human mind is not simply the user illusion that evolution theory dictates that it must be. How does Hoffman get around that?
Donald Hoffman: So I’ve used Evolutionary Game Theory to conclude that everything that we see around us in our perceptions is not vertical; it’s just a user interface, okay. and that means I have to go back and rethink what do. I mean ,what is the core of evolutionary theory that I can keep? I have to give up some physicalist assumptions that are typically made in evolution, okay? So most evolutionary biologists are also physicalists, of course. But it’s not absolutely necessary to be a physicalist to have the key principles of evolution… [6:08]
Note: Hoffman is offering a hope here, not a present reality. Darwinian evolution (the only currently respectable kind) is and always has been a physicalist theory. Physicalism is precisely what Darwinian evolution defends: mind from mud, via natural selection acting on random mutation. And, to be clear, the “mind” that the process creates is held to be a mere user illusion that enables the human
Robert Lawrence Kuhn: Yeah, but are you saying that consciousness was there before the process of evolution began? I, you know, I say that with a tremor in my voice. (6:13)
Donald Hoffman: That’s right. Absolutely so. For me to be entirely consistent, if I’m going to actually say that consciousness is fundamental, then I’m saying that the Big Bang itself is something that has to be understood from within a framework in which consciousness is fundamental. The standard view — and I understand that this is completely non-standard, what I’m saying — the standard view is that the Big Bang happened 13.7 billion years ago. Eventually, consciousness kind of arose accidentally here on Earth and maybe other places and totally accidentally, that’s right? So my story is completely different. (6:54)
Robert Lawrence Kuhn: So when I asked the question, how did consciousness emerge through an evolutionary process, your answer is it didn’t. (6:59)
Donald Hoffman: That’s right. Consciousness didn’t emerge from a prior physical process of evolution. Consciousness is fundamental and so we have to rethink the whole history of the universe actually from this point of view, from The Big Bang up through evolution. We have to rethink it in terms of how to rewrite that story, consistent with all of our current science but understanding that it’s … consciousness is fundamental, not the physical universe (7:23)
And, you know, one thing that comes out of this as well is, no one has been able to give a reason for why consciousness would evolve. What is it for? And so my attitude is, it didn’t evolve. It’s the ground from which evolution occurs. (7:38)
Note: Look what happened here: Hoffman starts by trying to align his consciousness theory with standard evolution theory and then just chucks that and says what he thinks: Consciousness didn’t evolve. It’s the ground from which evolution occurs. That’s surely defensible but it’s not, rest assured, the fully materialist theory taught, and enforced by law, in schools. The conflict between observation and accepted theory is one reason why consciousness is, as David Chalmers has put it, a “Hard Problem.“
organism to survive and spread selfish genes. Incidentally, dissenters from that one and only orthodox view have often been hounded from academic life.
Wednesday, 4 January 2023
Morphogenesis vs. Darwinism.
Diatoms and the Mystery of Morphogenesis
David Coppedge
From code to art: how does a linear set of instructions result in a beautifully crafted pattern? Diatoms do it, and scientists are struggling to figure out how. So far, they can see where spots of paint are appearing on the canvas, but the system that directs the finished masterpiece eludes them.
Morphogenesis is the construction of a functional shape from component parts. It’s a huge mystery in biology. It isn’t enough to accumulate the parts; they must be fit together according to an overall plan—in the right places, in the right order, and at the right time. Laufmann and Glicksman pointed out the mystery of bone morphogenesis in a sidebar on page 78 of Your designed body, comparing it to the construction of a house. “What does it take to build a house?” they ask; “Where are the shapes for these bones specified?”
Since bones are made by many individual (and independent) bone cells, building a bone is an inherently distributed problem. How do the individual bone cells know where to be, and where and how much calcium to deposit? How is this managed over the body’s development cycle, as the sizes and shapes of many of the bones grow and change? Surely the specifications for the shapes, their manufacturing and assembly instructions, and their growth patterns must be encoded somewhere. There must also be a three-dimensional coordinate systemfor the instructions to make sense. Is the information located in each bone cell, or centrally located and each individual bone cell receives instructions? If each bone cell contains the instructions for the whole, how does it know where it is in the overall scheme? How do all those bone cells coordinate their actions to work together rather than at odds with each other?
On a smaller scale, diatoms face (and solve) this same challenge. Instead of organizing cells together, they fit proteins and inorganic silica together. Diatoms have a blueprint (DNA) and a parts list (proteins) for construction of their glass houses. What drives them to create geometrical shapes from the parts, and place them in accurate positions in 3D space? This seems beyond the capabilities of parts and blueprints. It would be like placing a blueprint for a house on a pile of lumber, pipe, wire, and glass and expecting the house to self-organize. Even if a complete set of tools were available nearby, nothing would happen without foremen and skilled workers.
Diatom Houses
Valiant Effort
In a determined effort to understand how the diatom builds its glass house, a team from the Center for Molecular and Cellular Bioengineering in Dresden, Germany, attempted to identify the parts of the “silica deposition vesicle” (SDV) for T. pseudonana and determine how the protein machinery works to fit the “silica precursors” into their positions on the valve. Their results were published In PNAS by Christoph Heinz et al,“The molecular basis for pore pattern morphogenesis in diatom silica.
The magnitude of the problem can be appreciated in their introduction. The mystery of morphogenesis extends beyond diatoms, and understanding it could lead to revolutionary technologies.
Numerous organisms produce inorganic materials with amazingly complex morphologies and extraordinary properties in a process termed biomineralization. Prominent examples include the single-domain magnetite nanocrystals of bacteria that act as sensitive magnetic field sensors, the nacreous calcium carbonate layers of mollusks with exceptionally high fracture resistance, and the hierarchically porous, silica cell walls of diatomswith intriguing photonic properties. A fundamental understanding how genetically encoded machineries are capable of establishing physical and chemical forces that drive morphogenesis of such intricate mineral structures is currently lacking. Therefore, unveiling the mechanisms of biomineralization holds the promise of gaining advanced capabilities to synthesize minerals with tailored properties using environmentally benign processes.
This is all highly appetizing to consider, but reading their paper is like watching a Sherlock Holmes movie that never resolves: a plethora of clues, but no answer to the big question: who dunnit? “Come back later for the next exciting episode” is hardly satisfying.
Not that the authors didn’t try; they isolated the SDV, a first. They identified thousands of protein molecules in the SDV and searched for matched sequences in the UniProt database to sift the data down to the most likely candidates involved in pattern formation. After pinpointing some, they ran gene knockout experiments to see what resulted. They also identified receptors in the cell membrane for these proteins. Transporter proteins, ion pumps, silica transporters and other parts were labeled in a model diagram (Figure 5). They followed up on hypotheses that silica deposition involves liquid-liquid phase separation (LLPS), causing unassembled silica in the organic matrix to organize into “droplets” ready for deposition.
Proteomics analysis of the intracellular organelle for silica biosynthesis led to the identification of new biomineralization proteins. Three of these, coined dAnk1-3, contain a common protein–protein interaction domain (ankyrin repeats), indicating a role in coordinating assembly of the silica biomineralization machinery. Knocking out individual dank genes led to aberrations in silica biogenesis that are consistent with liquid–liquid phase separation as underlying mechanism for pore pattern morphogenesis.
Their model shows that dAnk1 appears to assemble the droplets, and dAnk2 and dAnk3 cooperate in stabilizing and disassembling them. But they never found the artist. The morpho genius behind morphogenesis remains unknown.
Origin of Morpho: First recorded in 1850–55; from New Latin Morphō, genus name, from Greek Morphṓ “the Shapely, the Beautiful” (an epithet of Aphrodite in Sparta), akin to morphḗ “form, shape, figure, beauty.”
Something Missing
The authors considered alternative hypotheses regarding the mechanism of pore pattern formation: is it template-driven or self-organizational? While finding that the dAnk1-3 genes “influence the morphogenesis of pore patterns,” no “morphogene” was found. This leads them to believe that “additional proteins and possibly other components are involved in the morphogenesis process.” But is this like looking for more tools lying around on a house construction site? Where is an entity that knows the master plan and understands how to carry it out?
Considerations such as this over many years led Michael Denton to reject genetic determinism and embrace structuralism: the philosophy that form precedes function, not vice versa. Biological structures arise from internal “laws of biological form,” he said in 2016, that are universal and built into the properties of matter.
On a personal note, it was my own increasing recognition that the gene-centric paradigm was failing at the cellular level and that the architecture of cells is an “epigenetic affair,” the result of the self-organization of cellular matter, which was one of the major factors influencing my own move to structuralism.
DENTON, EVOLUTION: STILL A THEORY IN CRISIS, P. 259.
Yet even structuralism seems to be missing something. There is no law of biological form that necessarily makes it self-organize into a five-pointed star or a triangle, else all diatoms would look the same. Thousands of other species within the same environment inherit very different shapes. There is no material law that could take a form like a five-pointed star and encode it into a genome that leads to consistent inheritance of that form in its progeny. Structuralism might explain snowflakes, which though profoundly unique, are nevertheless built on the same structural pattern inherent in ice crystals. Snowflakes, are also not inherited from a linear code, as in biology. The organizing principles in biological structures seem very different from any other examples of self-organization in nature.
Software in the Hardware
The only mechanism we know for sure can faithfully reproduce a form from a linear code is software. A designing intelligence that writes software does not have to be present when it is operating. A 3D printer can run automatically, producing unlimited copies of a shape, given sufficient supply of resin. If a toy shop were running software-directed morphogenesis, no amount of inspection of the properties of the resin and machinery would predict the shape of a statuette coming out. The shape was in the mind of the programmer, not in the properties of the ingredients, the laws of nature, or the environment.
More Design in Diatoms
Two other facts about diatoms should arouse our appreciation of their intelligent design. One is that another atomic element — silicon — has found its way into the periodic table of biology. See our other articles about elements in life: phosphorus, boron, potassium, and about 20 others. The finely-tuned properties of elements have been detailed by Michael Denton in The Miracle of Man and his other “Privileged Species” books and videos. Diatoms could have taken on plain shapes without silica shells and still survive, as do other plankton. But the world is enriched by their crystalline architectures.
Another awesome fact about diatoms is their contribution to animal life. Diatoms produce about 25 percent of the air we breathe. This raises a philosophical puzzle of how necessary things can also be beautiful. Would we expect a statue in a museum to sweep its own floor? A healthy atmosphere might come from amorphous blobs of photosynthetic organisms, but the beauty of diatoms adds artistry to function.