Sunday, 25 August 2024
Yet more re:Darwinian occultism
Will Evolution’s New Synthesis Be Hard or Soft Magic?
The popular fantasy novelist Brandon Sanderson likes to divide magic into two categories: “soft magic” and “hard magic.”
In a hard magic system, the rules of the magic are made explicit to the reader: If you do x, y happens. If Harry Potter points his magic wand at someone and says, “Stupify!” then that person will be knocked unconscious.
In a “soft” magic system, by contrast, everything is left vague. If Gandalf raises his staff and hollers, then…something will happen. Possibly.
Sanderson points out that soft magic is best used for creating a sense of awe and wonder, while hard magic is best used for moving the plot forward and solving problems. Hard magic is not ideal for stirring up those magical feelings, because there is less mystery involved. Soft magic is not good for moving the plot, because if the reader doesn’t understand how the magic works, using it to solve the characters’ problems will feel like cheating.
This leads to Sanderson’s First Rule of Magic: An author’s ability to solve conflict with magic is DIRECTLY PROPORTIONAL to how well the reader understands said magic.
For example, this is why J. R. R. Tolkien had to keep Gandalf well out of the way for the most crucial parts of his plots. If Tolkien had made Gandalf simply magic the ring into the fires of Mount Doom and save the day, the readers would have lost interest.
Some scientists could stand to apply Sanderson’s First Rule.
These days, quite a few biologists are saying that the neo-Darwinian synthesis has failed as an explanation for life. The magic just isn’t working anymore. There’s a lot of talk about a new synthesis to replace it. Ideas like emergence, self-organization, self-construction, panpsychism, teleonomy, and more are being put forward.
The question is: Will this new synthesis be soft magic, or hard?
Darwin’s Hard Magic
Darwin’s theory, for all its flaws, was “hard magic.” It had clearly defined rules: Self-reproducing organisms experience tiny, random variations. The beneficial ones accumulate over (practically limitless) time. This causes the organisms to slowly diversify into countless species, with each one suited to its environment.
It was clear what this could explain, and what it couldn’t. For example, it could explain the gradual diversification of the species, but not the origin of life, or any sudden changes in the fossil record.
Because the rules were clear, the explanation was satisfying to many people. The only problem was that it didn’t take into account some things Darwin didn’t know:
First, it turned out that the universe is probably not eternal. Darwin didn’t know that.
Second, DNA and the genetic basis of “random variation” were discovered, and it became possible to compare the amount of time needed to have a reasonably high chance of getting a given variation with the time actually available to get it.
Third, better microscopes revealed the mind-boggling sophistication of life at the molecular level.
Fourth, tying all these together, the molecular biologist Michael Behe noticed that many molecular structures are characterized by a high level of interdependency among parts, meaning that tiny changes on the path to creating one of these structures would not yield any survival advantage (and therefore not be selected for) until the whole structure was complete. He ran the math on the number of mutations you would need to get a typical complex feature functioning (and therefore visible to natural selection), and found that quite literally all the time in the world is not enough.
Darwin’s theory was well-formulated and explicit. He just didn’t understand what we do now.
The Hard Magic of ID
I would say that evolution’s oldest rival, intelligent design, is also in a sense “hard magic.”
That may be a surprising assertion. If the designer is God, per Stephen Meyer’s Return of the God Hypothesis, God is certainly a Gandalf-like figure who can do whatever he wants. (Correction: Gandalf is a God-like figure.) In fact, that is one of the main criticisms of ID: that because God is inherently unpredictable, you can’t legitimately do science on him.
This is correct, actually. There can never be a formal science of God, or even a science that says definitively when some effect was caused by God and when it wasn’t. God — by definition — can do whatever he wants. Unlike natural phenomena, he has no limits, and therefore cannot be studied as a natural phenomenon.
But intelligent design is the study of design, not of God.
It’s possible to infer that something was designed, and this inference can be made mathematically rigorous, given enough data. This is not even controversial; the design inference is applied to non-deific minds in many uncontroversial fields, such as forensics, despite the facts that human minds are not much better understood by science than God’s mind is.
That’s because, while minds are not well understood, one of the only things we do understand about them is that they can design things that would not have otherwise arisen by chance and contingency, and that they do this to achieve goals. Based on this (universal) observation, intelligent design posits that if something has a specified, identifiable function, then the likelihood it was designed by a mind is the inverse of the likelihood that it arose by chance and contingency.
But that doesn’t mean that ID theory can say who the designer was. Forensics can’t tell you whether a person or a supernatural genie of infinite power murdered someone. (You can find DNA, but the genie could have faked it.) But it can tell you that they didn’t die by chance. Whether a murderer or a devious genie is more likely is a question for philosophy. Likewise, mathematical analysis of proteins can’t tell you whether those proteins were designed by God, or a genie, or Jack the Ripper. But it most certainly can tell you that the proteins didn’t emerge by chance.
Gandalfing the Ring into Mount Doom
So much for Darwinism and ID. What about the new contenders to replace/modify neo-Darwinism?
Well, they’re certainly good at creating magical feelings.
Take the self-construction theorist Stuart Kauffman, waxing poetic on the theory. He says:
I invite you to do something. Go into a forest, by yourself — with some animals and some plants and some bacteria and stuff — and look around and say, “All that’s happened is that for the past 3.5 billion years the sun’s been shining, there’s been a few other sources of free energy, and all this stuff came to exist with nobody in charge.” That’s true. How much do you want for God? It’s so awesome, mysterious, grand. That’s God enough for me.
It is indeed a very cool feeling. For me, it’s similar to the feeling I get watching Mickey Mouse struggle with the animated brooms in Fantasia. Very magical.
It cannot, however, “move the plot.”
How, exactly, do these theories make the emergence of life more likely than by chance? And by how much more likely? What are the odds of any specific feature emerging through teleonomy, synergism, self-organization, self-construction, autopoiesis, or emergence? How would one go about calculating these odds?
Hard to say.
It seems that kind of math Behe applied to neo-Darwinism simply can’t be applied to the new theories, because there is nothing solid to run the numbers on. To the extent that hard details are actually given, you usually find that the scientist is either (1) sneaking in an unexplained mind (for example, positing unaccounted-for intelligence in bacteria), or (2) merely describing the developing sophistication of life without actually accounting for it.
Of course, it’s only fair to expect that an idea will start out vague. Even Darwin’s theory didn’t become really “hard” until it was integrated with Mendelian genetics after his death. I hope that these new hypotheses will be filled out with concrete details soon. Then they can become actual competitors with neo-Darwinism and ID.
But until that happens, they will continue to leave their intended audience unsatisfied. Even in a fantasy novel, you need to do better than that.
Friday, 23 August 2024
The struggle to replant Darwinism's tree of life is real?
Fossil Friday: The Mystery of the Frankenstein Dinosaur
This Fossil Friday we will look at a paleontological enigma that reveals a lot about the weaknesses of reconstructions of evolutionary trees and the phylogenetic classification of organisms, based on such shaky tree reconstructions. Paleobiologists use a methodology called cladistic analysis to reconstruct the assumed evolutionary relationships of fossil organisms. Of course, this cladistic methodology makes certain unproven assumptions such as the principle of parsimony and bifurcating (dichotomous) branching, even though nature is under no obligation to favor the most parsimonious trees or to avoid polytomous branchings or even network-like relationships (e.g., due to hybridization). But anyway, here is in simple words how cladistic tree reconstruction works in principle.
How It Is Done
The scientists compile a list of observable and relevant anatomical features of a fossil organism and possible fossil and living relatives. They construct a spread-sheet-like data matrix with different taxa as rows and different characters as columns. The fields of this data matrix allow for the coding of all character states for every taxon. These character states are usually coded as 0 for absent (or primitive / plesiomorphic state) and 1 for present (or derived / apomorphic state). Then a computer algorithm is used to find the most parsimonious branching pattern of a phylogenetic tree, which best explains the distribution of character states in the data matrix with the minimal number of necessary steps for evolutionary gains and losses. A so-called out-group taxon is included in the analysis, which is either a taxon that is presumed to be certainly more distantly related than all the other included taxa to each other, or is a hypothetical ancestor, which is coded with 0 for all character states. The tree is rooted in a way that this out-group represents the first branching of the tree. Only groups that include all branches of a node are recognized in the phylogenetic classification as monophyletic groups or clades, while grades of transitional series (paraphyletic groups) or polyphyletic groups that do not share a unique common ancestor are rejected as artificial groupings. This is why modern classifications no longer include taxa like invertebrates, or fish, or reptiles. The attribution of a fossil to a certain group must only be based on so-called shared derived characters (synapomorphies) but not on primitive similarities (symplesiomorphies) or convergent similarities (homoplasies).
So Far So Good
Now, given that we have a very extensive knowledge of most groups of dinosaurs, what would you expect if we find a new dinosaur that is almost completely and well preserved. Shouldn’t we be quite easily able to place it in the existing phylogenetic system based on the observed putative synapomorphies, thus the shared derived similarities with already known forms? Well, this works in happy Darwinian fantasy land of text books and the propaganda of popularizers of Darwinism like Richard Dawkins and Jerry Coyne, but the reality is up for a crude awakening. Often new discoveries show a confusing combination of characters that either overturn the previously preferred phylogenetic trees or require numerous ad hoc hypotheses to explain away the conflicting characters. Here is a very good example:
A few years ago, a new dinosaur genus and species, named Chilesaurus diegosuarezi, was described after a rather complete skeleton from the Late Jurassic of Chile (Novas et al. 2015). This dinosaur roamed Patagonia about 147-148 million years ago (Suárez et al. 2015). Actually, several isolated bones were already discovered and described previously, but erroneously considered to belong to different dinosaur taxa because they look so totally unrelated (Salgado et al. 2008, 2015). The original describers realized that the new dinosaur represents a quite enigmatic taxon with a bizarre combination of traits (Novas et al. 2015), and others called it “one of the most puzzling and intriguing dinosaurs ever discovered” (Barrett quoted in Rahim 2017). Initially, it was considered to be a derived theropod (Novas et al. 2015, Chimento et al. 2017, Lenin-Chávez et al. 2017, Cau 2018), thus a relative of the bipedal carnivorous dinosaurs, in spite of its spatulate dentition that clearly suggests a plant-eater (also see Lemonick 2015). It was even suggested that the forelimb structure foreshadows the acquisition of flight adaptations in avian theropods (Chimento et al. 2017). The very same year, a new study by Baron & Barrett (2017) suggested a very different affinity as basal ornithischian and a transitional ‘missing link’ between Ornithischia and Theropoda (University of Cambridge 2017). This was celebrated by media head lines around the globe as a final solution of the “mystery of the Frankenstein dinosaur” (Anonymous 2017, Geggel 2017, Gosh 2017, Rahim 2017).
One Year Later
However, just another year later a new study by Müller et al. (2018) disagreed and suggested that Chilesaurus was instead a basal representative of the sauropod lineage, but also cautioned that:
… these results demonstrate how search parameters, character scoring and taxon sampling could affect the phylogenetic position of C. diegosuarezi. Accordingly, our replication of Baron & Barrett’s [1] is compelling evidence that the phylogenetic status of C. diegosuarezi remains unstable and the mystery of this enigmatic dinosaur still remains unsolved.
Baron & Barrett (2018) defended their hypothesis, and subsequently, Müller & Dias-da-Silva (2019) changed their mind in a new study and now agreed that Chilesaurus is the basal-most member of Ornithischia, but again cautioned about unstable branches and “great uncertainty about the basic structure of the dinosaur family tree.”
A more recent study by Norman et al. (2022) recovered Chilesaurus as a highly derived ornithischian deeply nested in the family Heterodontosauridae. However, the authors also commented:
The ‘missing-link’ interpretation of its placement (Baron & Barrett, 2017) is incongruent chronologically (Late Jurassic) and evolutionarily, in the context of the acquisition of the fundamental ornithischian bauplan, but its curious opisthopubic pelvic anatomy may point toward either iterative (the repeated theropodan acquisition of opisthopuby) or atavistic anatomical phenomena. It is clear that the relationship of Chilesaurus in Dinosauria needs clarification. Most recently, Federico Agnolín (pers. comm., 25 April 2022) has reaffirmed the theropod affinities of Chilesaurus on the basis of the presence of pleurocoels, complex laminae on the cervical vertebrae, the shape of the ilium and carpal anatomy
Baron (2022) admitted that “despite these recent fluctuations, the original placement within Theropoda remains the most prevalent phylogenetic hypothesis” and that the results of his new “analysis do not by any means end the debate”, but claimed that it “produced results that again suggest that Chilesaurus could be an early diverging member of Ornithischia.” I suggest our confidence in this “could” should not be too high.
A Complete Revolution?
Of course, it is also interesting in this context that the working group of Matthew Baron and Paul Barrett published a sensational new Ornithoscelida-hypothesis of dinosaur relationships (Baron et al. 2017), which suggested a complete revolution of the traditional division of dinosaurs into those with lizard-like hips (Saurischia) and those with bird-like hips (Ornithischia). Needless to say, the new phylogeny is still highly controversial and was quickly met with some support (Cau 2018, Müller & Dias-da-Silva 2019) but also with strong skepticism and criticism by proponents of the classical hypothesis (Müller & Garcia 2020, Novas et al. 2021), which ruled dinosaur classification since 1888. Curiously, the feathered non-avian theropods and birds do not belong to the clade with bird-like hips in either hypothesis, which is quite telling in itself. Actually, the disagreement is even worse, as was convincingly shown by Norman et al. (2022: fig. 1), who documented that basically every possible topology of the relationships between the three major groups of dinosaurs has be advocated by some modern experts (see the image below).
The Collapsing Tree Challenge
This mess is yet another confirmation of my collapsing tree challenge to neo-Darwinists (Bechly 2024). Phylogenetics very much looks like a pseudoscience (such as astrology or homeopathy) with a very sophisticated methodology, which fails to produce any consistent results. Different studies based on different data do not converge on one true tree of life. When Darwin sketched his famous first tree of life in his notebook, he titled it “I think.” Maybe he would think again today. We definitely should!
References
Anonymous 2017. Monster mash: does the Frankenstein dinosaur solve the mystery of the Jurassic family tree? The Guardian August 16, 2017. https://www.theguardian.com/science/shortcuts/2017/aug/16/frankenstein-dinosaur-chilesaurus-diegosuarezi-mystery-jurassic-family-tree
Baron MG 2022. The effect of character and outgroup choice on the phylogenetic position of the Jurassic dinosaur Chilesaurus diegosaurezi. Palaeoworld 33(1), 142–151. DOI: https://doi.org/10.1016/j.palwor.2022.12.001
Baron MG & Barrett PM 2017. A dinosaur missing-link? Chilesaurus and the early evolution of ornithischian dinosaurs. Biology Letters 13(8):20170220, 1–5. DOI: https://doi.org/10.1098/rsbl.2017.0220
Baron MG, Norman DB & Barrett PM 2017. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature 543(7646), 501–506. DOI: https://doi.org/10.1038/nature21700
Baron MG & Barrett PM 2018. Support for the placement of Chilesaurus within Ornithischia: a reply to Müller et al. Biology Letters 14(3):20180002, 1–2. DOI: https://doi.org/10.1098/rsbl.2018.0002
Bechly 6 2024. Fossil Friday: Three Modern Scientific Challenges to the Causal Adequacy of Darwinian Explanations. Evolution News May 17, 2024. https://evolutionnews.org/2024/05/fossil-friday-three-modern-scientific-challenges-to-the-causal-adequacy-of-darwinian-explanations/
Cau A 2018. The assembly of the avian body plan: a 160-million-year long process. Bollettino della Società Paleontologica Italiana 57(1), 1–25. https://www.researchgate.net/publication/324941372 [DOI is broken]
Chimento NR, Agnolin FL, Novas FE et al. 2017. Forelimb Posture in Chilesaurus diegosuarezi (Dinosauria, Theropoda) and Its Behavioral and Phylogenetic Implications. Ameghiniana 54(5), 567–575. DOI: https://doi.org/10.5710/amgh.11.06.2017.3088
Geggel L 2017. This Enigmatic Dinosaur May Be the Missing Link in an Evolution Mystery. LiveScience August 16, 2017. https://www.livescience.com/60150-dinosaur-family-tree-missing-link.html
Ghosh P 2017. ‘Frankenstein dinosaur’ mystery solved. BBC August 16, 2017. https://www.bbc.com/news/science-environment-40890714
Lemonick MD 2015. T. rex’s Oddball Vegetarian Cousin Discovered. National Geographic April 27, 2015. https://web.archive.org/web/20150429185152/http://news.nationalgeographic.com/2015/04/150427-theropod-dinosaur-vegetarian-rex-science/
Lenin-Chávez C, Ocampo-Cornejo P & Manzanero E 2017. Depicting Chilesaurus diegosuarezi (Dinosauria, Theropoda). Conference poster. https://www.researchgate.net/publication/376409197
Müller RT & Dias-da-Silva S 2019. Taxon sample and character coding deeply impact unstable branches in phylogenetic trees of dinosaurs. Historical Biology 31(8), 1089–1092. DOI: https://doi.org/10.1080/08912963.2017.1418341
Müller RT & Garcia MS 2020. A paraphyletic ‘Silesauridae’ as an alternative hypothesis for the initial radiation of ornithischian dinosaurs. Biology Letters 16(8):20200417, 1–5. DOI: https://doi.org/10.1098/rsbl.2020.0417
Müller RT, Augusto Pretto F, Kerber L, Silva-Neves E & Dias-da-Silva S 2018. Comment on ‘A dinosaur missing-link? Chilesaurus and the early evolution of ornithischian dinosaurs’. Biology Letters 14(3):20170581, 1–2. DOI: https://doi.org/10.1098/rsbl.2017.0581
Norman DB, Baron MG, Garcia MS & Müller RT 2022. Taxonomic, palaeobiological and evolutionary implications of a phylogenetic hypothesis for Ornithischia (Archosauria: Dinosauria). Zoological Journal of the Linnean Society 196(4), 1273–1309. DOI: https://doi.org/10.1093/zoolinnean/zlac062
Novas F, Salgado L, Suárez M et al. 2015. An enigmatic plant-eating theropod from the Late Jurassic period of Chile. Nature 522(7556), 331–334. DOI: https://doi.org/10.1038/nature14307
Novas FE, Agnolin FL, Ezcurra MD, Müller RT, Martinelli A & Langer M 2021. Review of the fossil record of early dinosaurs from South America, and its phylogenetic implications. Journal of South American Earth Sciences 10:103341. DOI: https://doi.org/10.1016/j.jsames.2021.103341
Rahim Z 2017. ‘Frankenstein dinosaur’ enigma solved. CNN August 16, 2017. https://edition.cnn.com/2017/08/16/health/frankenstein-dinosaur-chilesaurus/index.html
Salgado L, De La Cruz R, Suárez M, Gasparini Z & Fernández M 2008. First Late Jurassic dinosaur bones from Chile. Journal of Vertebrate Paleontology 28(2), 529–534. DOI: https://doi.org/10.1671/0272-4634(2008)28[529:FLJDBF]2.0.CO;2
Salgado L, Novas FE, Suarez M, De La Cruz R, Isasi M, Rubilar-Rogers D & Vargas A 2015. Late Jurassic Sauropods in Chilean Patagonia. Ameghiniana 52(4), 418–429. DOI: https://doi.org/10.5710/amgh.07.05.2015.2883
Suárez M, De La Cruz R, Fanning M, Novas F & Salgado L 2015. Tithonian age of dinosaur fossils in central Patagonian, Chile: U–Pb SHRIMP geochronology. International Journal of Earth Sciences 105(8), 2273–2284. DOI: https://doi.org/10.1007/s00531-015-1287-7
University of Cambridge 2017. Study identifies dinosaur ‘missing link’. University of Cambridge press release August 16, 2017. https://www.cam.ac.uk/research/news/study-identifies-dinosaur-missing-link
Thursday, 22 August 2024
Monday, 19 August 2024
Sunday, 18 August 2024
A gift from the heavens?
The Story of Metals Points to Nature’s Foresight, Planning, Preparation
A confluence of conditions conspired to bring metals to Earth and make them accessible to humans. But can a Darwinian process take the credit? On a new episode of ID the Future, I conclude a two-part conversation with Eric Hedin, professor emeritus of physics and astronomy at Ball State University.
In Part 2, Dr. Hedin begins by reviewing the cosmic origins of our heavy metal minerals, including iron, copper, bronze, gold, silver, platinum, and others. He also reminds us of the beneficial interaction between metals and microbes that makes advanced life on Earth possible. Hedin describes the conditions within ourselves and the conditions within our environment that were finely tuned to allow for our successful utilization of metals. He also speaks to what our use of metals reveals about the moral character of human nature.
Hedin explains why our dependence on metals continues to this day. The development of technologies associated with consumer electronics, renewable energy, and specialty steel have sparked demand for a range of specialty mineral commodities that just happen to be available for human extraction from the Earth’s crust. Hedin argues that the finely tuned confluence of conditions that brought us metals cannot be chalked up to a Darwinian process. Instead, the story of metals points to foresight, planning, and preparation, hallmarks of an intelligent design at work in the cosmos.
Find the podcast and listen to it here.
Part 2 of a two-part conversation. Listen to Part 1 here.
Saturday, 17 August 2024
The engineered hard power of soft roots vs. Darwin.
How Roots Become Jackhammers
Many of us have wondered how seedlings get into the smallest cracks in driveways and sidewalks, finding openings and then penetrating hard layers to reach sunlight. In time, the seemingly flimsy shoots can cause the asphalt or concrete to buckle! Homeowners know that without stopping this natural process in time, a driveway can become a field of weeds. It’s amazing to think that such delicate stems, without muscles, can penetrate hard surfaces that greatly exceed their own strength.
A similar thing happens down at the tips of roots. A growing root tip may encounter a layer of hardpan that blocks its progress. It can either bend sideways or remain in place and call in its team of jackhammers. How it does that was the subject of a paper in Current Biology by 11 researchers, mostly from China, who want to know how to increase rice crops on which many people around the world depend for food. Rice farmers can try to plow the soil to loosen it up, which is very work intensive on terraced hillsides. An alternative would be to genetically modify the plant’s own built-in jackhammers to increase their ability to penetrate whatever soil they encounter
High School Lab Work with University Finesse
Those of us who experimented with bean sprouts in high school, watching how they grow in response to light and gravity, can relate to parts of this paper. The researchers grew rice seedlings in agar dishes and photographed their progress. Like us, they also experimented with auxin, a common plant growth hormone. What we never did in high school, though, was to genetically modify hormones with green fluorescent protein or determine the specific genes involved in root growth. Only grad level research gets that heavy into experimentation. The team also determined specific proteins involved in the “jackhammer” process and grew mutant strains lacking them to compare with the wild type (WT) seedlings. Their results were simple yet profound.
For controls, they filled agar dishes with soft (1 percent) agar and hard (3 percent) agar halfway down, simulating a hardpan layer that a root tip would encounter as it grows. One intuitive finding was that a root tip approaching the hard layer has a better chance of penetrating it if it approaches it at a right angle (90°). Gravitropism generally takes care of that. A protein named “auxin influx carrier AUXIN RESISTANT 1” (OsAUX1) was implicated in keeping the root tip pointed down. They found this out by creating a mutant form osaux1-3 lacking its function.
How can OsAUX1 facilitate root penetration into harder layers? OsAUX1-mediated shootward auxin transport is required for root gravitropism and root hair elongation in response to environmental stimuli. Consistently, osaux1-3 exhibits a reduced gravitropic response, as evidenced by a bending angle of approximately 30°, in contrast to the approximately 90° exhibited by the WT (Figures S1A and S1B). The osaux1-3 mutant also displays shorter root hairs (but with a normal number of root hair) in the split system compared with the WT (Figures S1C–S1H), indicating that the elongation of root hair in response to encountering a harder layer is dependent on OsAUX1.
Root Hairs as Anchor Bolts
Here the experiments get interesting. OsAUX1 plays two roles: keeping the root tip oriented downward and signaling for more root hairs to grow. The root hairs grow out horizontally from the root farther above the tip. Images of root tips with green fluorescent protein (GFP) show flows of auxin rising from the tip, where OsAUX1 triggers root hairs to produce more auxin. As a result, the root hairs grow longer, where they can anchor the main root in position. If you think of a jackhammer not being firmly held by an operator, it would bounce on the concrete instead of penetrating it. It needs to be anchored. Similarly, root hairs growing outward into the surrounding soil anchor the main root in position.
Root hairs are reported to aid seedling establishment through providing anchorage for emerging roots to penetrate the soil surface. Quantification of the maximum reaction force (anchorage) provided by root hairs is frequently based on the force required to extract a root. In uniform systems, the force needed to pull out a WT root was significantly greater than that required for root hair mutants across different densities of agar layers (Figure S5). Our findings support that increased root hair lengths enhance the anchorage of growing root tips to penetrate harder layers.
Root hairs are extremely thin and tiny, but enough of them spread out in all directions are sufficient to hold the main root in position for its task of penetrating the hard layer. As we learned in high school, root hairs are important for increasing the sampling area of soil for nutrient exploration. Another vital task they perform was mentioned in the paper: acquiring phosphate. As I wrote here, phosphorus is often a limiting factor for biological productivity.
The elongation of root hair results in an increased surface area of root-soil contact, generating the required anchorage force to support root penetration into compacted layers. Our previous research has also unveiled the pivotal role of OsAUX1 in facilitating root hair elongation under low phosphate conditions. This process is crucial for transporting auxin back to the differentiation zone, where root hair elongation takes place. This finding underscores the possibility that longer root hair in compacted soil may have contributed to enhanced phosphate uptake.
Accessory Proteins Essential Too
Engineering foresight took care of another problem. If the root tip grew at a constant rate when encountering the hard layer, it would likely buckle or bend. And so, as if knowing this possibility in advance, an impedance switch was built into the system. The impedance of hardpan triggers another protein, OsYUC8, to go into action switching on auxin synthesis at the root tip. OsAUX1 is then carried by transporters up to the root hairs where they also start producing more auxin, growing longer for better anchoring and nutrient exploration.
How does contact with hardpan switch this activity on? The slowdown of the root tip apparently is triggered by our friend PIEZO1 (discussed here), the touch-sensitive protein.
The mechanistic basis of OsYUC8 upregulation after encountering mechanical impedance remains unclear (Figure 2). Mechanical stimulation induces higher expression of the mechano-inducible calcium channel PIEZO1(PZO1) in columella and lateral root cap cells in Arabidopsis. Furthermore, pzo1 seedlings exhibited reduced calcium transients and failed to penetrate hard agar, indicating the involvement of PZO1 in the root’s short-term response to mechanical detection of compacted soil layers. This calcium-signaling pathway may act upstream of auxin (and OsYUC8) in the root barrier-touching response.
As usual, additional players take part in this process, increasing the complexity of the system. There are 13 other OsYUC proteins, as well as other genes, promoters, hormones, and tissues discussed in the paper. This brief overview, however, gives a taste of what’s needed for a rice root to grow in hard soil. The plant has to switch on numerous signals, transporters and promoters to slow the root down, build up the anchors in the soil, and with added auxin growth hormone, begin a controlled penetration by the tip through the hardpan. All this for a single root facing a challenge. When it succeeds, the root can explore deeper for the nutrients it needs and be more likely to survive dryness at the surface.
Not Just Rice
The authors realize that similar processes are built into other plants. Their opening sentence says, “Compacted soil layers adversely affect rooting depth and access to deeper nutrient and water resources, thereby impacting climate resilience of crop production and global food security.” Pretty important. Knowing now what they have learned — without relying on evolutionary theory even once — they can offer hope to a needy world. Their ending sentence says, “Our results provide new insights into a key root trait for breeders to select to enable crops to be more resilient to soil stresses by exploiting variation in root hair length.”
“For breeders to select” — that’s intelligent design.
Friday, 16 August 2024
More on why neanderthal Man is disinherited no more.
Fossil Friday: Human Nature of Neanderthals Supported Again
In a recent Fossil Friday article (Bechly 2024) I discussed the many lines of evidence that have accumulated in the past decade in favor of a fully human nature of Neanderthal men. As I documented with many references to the most up-to-date peer-reviewed research, we know that Neanderthals used fire, buried their dead, created stone circles and bone tools, made jewelry from eagle talons and used feathers as body decoration, made cave art with paintings and engravings, played music with bone flutes, used ochre as pigment and sophisticated fiber technology, produced flour from processed plants, dived for seafood, cooked food and self-medicated with herbal painkillers and antibiotics, and even produced glue from birch bark with a complex chemical procedure.
Hints of Compassion
Now, we can add compassion to this growing list of very human behaviors. A new study by Conde-Valverde et al. (2024) described fragments of hominin fossils from the Cova Negra cave in Spain, which have been dated by electron spin resonance (ESR)/U-series to an age of 273-146 thousand years ago. The age and the morphology clearly suggest an attribution to Neanderthals. But the truly remarkable finding was that the remains of a six-year-old child showed the typical congenital pathologies of the inner ear associated with debilitating Down syndrome. The authors suggest that this disabled child “would have required care for at least 6 years, likely necessitating other group members to assist the mother in childcare.” The press release emphasized that this “Fossil of Neanderthal child with Down’s syndrome hints at early humans’ compassion” (Reuters 2024).
It was known already that Neanderthals cared for sick and injured individuals (Hublin 2009, Noble 2010, Spikins et al. 2010, 2018, Tilley 2015, 2022, Thorpe 2016, Spikins 2022), but such behavior can also be found in some of the more intelligent and social animal species like the great apes, elephants, and whales. However, extended caregiving for a strongly disabled child is a highly non-Darwinian behavior that indeeds suggests compassion on a level only found in humans, because it is not driven by mere survival of the fittest and differential reproductive success. Elephants abandon or even kill disabled infants (Rodrigo 2011). Monkeys and apes usually neglect or reject disabled infants (Hogenboom 2015), or at best bother to care for a few weeks (Jackson 2023, Valença & Falótico 2023). There exists just a single report of maternal care for a 23-months-old disabled chimp infant with symptoms similar to Down syndrome (AFP 2015, Matsumoto et al. 2016). The compassionate caregiving of Neanderthals is clearly not intermediate between such animal behaviour and human behavior, but rather as Noble (2010) put it: Modern research “rejects the popular portrayal of Neanderthals as simple, unfeeling brutes and suggests that our closest ancient relatives may well have demonstrated a level of compassion that would put many modern humans to shame, caring for the infirm and the vulnerable for years at a time in organised groups.”
Strongly Corroboration
As I discussed in my previous article (Bechly 2024), the strong evidence for significant and common genetic admixture with modern humans, also suggests that Neanderthals and modern humans belonged to the same species. This was recently strongly corroborated by a new genetic study published in the journal Science (Li et al. 2024; also see Choi 2024b and Starr 2024), which found clear evidence for a “recurrent gene flow between Neanderthals and modern humans over the past 200,000 years”, suggesting a decreasing Neanderthal population that “was ultimately being absorbed into the modern human gene pool” as already suggested by a previous study (Stringer & Crété 2022). This definitely goes far beyond just some rare instances of admixture. Instead, it confirms a shared gene pool of different subpopulations within the same biospecies. Neanderthals were not a separate species of primitive hominins that went extinct, but were one of us and are still with us in our genes. They only vanished as a distinct group just like many other ancient subpopulations of humans, such as the Jomon people in Japan.
A Somewhat Different Result
Strangely, another new genetic study by Iasi et al. (2024), which is still in preprint stage and not yet peer-reviewed, comes to a somewhat different result and “suggests that humans interbred with Neanderthals 47,000 years ago for a period lasting 6,800 years” (Choi 2024a), but that “interbreeding that occurred at other times, such as the earlier events that impacted the Neanderthal genome, likely did not leave a detectable trace in our genome” (Choi 2024b). Looks like there is still much room for disagreement and different interpretation of the data, leading to quite different speculative scenarios.
Anyway, neither compassionate human behavior nor a shared gene pool would by itself refute a Darwinian evolution of modern humans, but such evidence certainly better resonates with the views of Darwin critics, who have always championed the view that there is only one humankind and that it is unique and distinct from the animal kingdom. Neanderthals and other ancient representatives of our genus Homo are not “stepping stones” on the way from bacteria to Beethoven, but just examples of human diversity in space and time.
References
AFP 2015. Japan researchers find chimps caring for disabled infant. Phys.org November 11, 2015. https://phys.org/news/2015-11-japan-chimps-disabled-infant.html
Bechly G 2024. Fossil Friday: New Evidence for the Human Nature of Neanderthals. Evolution News February 2, 2024. https://evolutionnews.org/2024/02/fossil-friday-new-evidence-for-the-human-nature-of-neanderthals/
Choi C 2024a. Neanderthals and humans interbred 47,000 years ago for nearly 7,000 years, research suggests. LiveScience June 7, 2024. https://www.livescience.com/archaeology/neanderthals-and-humans-interbred-47000-years-ago-for-nearly-7000-years-research-suggests
Choi C 2024b. Neanderthals didn’t truly go extinct, but were rather absorbed into the modern human population, DNA study suggests. LiveScience July 11, 2024. https://www.livescience.com/health/genetics/neanderthals-didnt-truly-go-extinct-but-were-rather-absorbed-into-the-modern-human-population-dna-study-suggests
Conde-Valverde M, Quirós-Sánchez A, Diez-Valero J, Mata-Castro N, García-Fernández A, Quam R, Carretero JM, García-González R, Rodríguez L, Sánchez-Andrés Á, Arsuaga JL, Martínez I & Villaverde V 2024. The child who lived: Down syndrome among Neanderthals? Science Advances 10(26):eadn9310, 1–10. DOI: https://doi.org/10.1126/sciadv.adn9310
Iasi LNM, Chintalapati M, Skov L, Bossoms Meta A, Hajdinjak M, Peter BM & Moorjani P 2024. Neandertal ancestry through time: Insights from genomes of ancient and present-day humans. bioRxiv May 13, 2024. DOI: https://doi.org/10.1101/2024.05.13.593955
Hogenboom M 2015. The wild chimpanzee who cared for her child with disability. Projeto GAP November 17, 2015. https://www.projetogap.org/en/news/the-wild-chimpanzee-who-cared-for-her-child-with-disability/
Hublin J 2009. The prehistory of compassion. PNAS 106(16), 6429–6430. DOI: https://doi.org/10.1073/pnas.0902614106
Jackson J 2023. Compassionate disabled infant care from a wild capuchin monkey mother. Phys.org March 7, 2023. https://phys.org/news/2023-03-compassionate-disabled-infant-wild-capuchin.html
Li L, Comi TJ, Bierman RF & Akey JM 2024. Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 385(6705), 1–10. DOI: https://doi.org/10.1126/science.adi1768
Matsumoto T, Itoh N, Inoue S & Nakamura M 2016. An observation of a severely disabled infant chimpanzee in the wild and her interactions with her mother. Primates 57, 3–7. DOI: https://doi.org/10.1007/s10329-015-0499-6
Noble C 2010. My bright idea: Neanderthals could show compassion. The Guardian October 10, 2010. https://www.theguardian.com/technology/2010/oct/10/bright-idea-neanderthals-evolution
Reuters 2024. Fossil of Neanderthal child with Down’s syndrome hints at early humans’ compassion. The Guardian June 26, 2024. https://www.theguardian.com/science/article/2024/jun/26/fossil-of-neanderthal-child-with-downs-syndrome-hints-at-early-humans-compassion
Rodrigo M 2011. Handicapped baby jumbo left bleeding and abandoned in paddy field. Sunday Times May 1, 2011. https://www.sundaytimes.lk/110501/News/nws_28.html
Spikins P 2022. Material evidence: Caring for adult vulnerabilities. pp. 71–127 in: Hidden Depths: The Origins of Human Connection. White Rose University Press, New York (NY). DOI: https://doi.org/10.22599/HiddenDepths.c
Spikins P, Rutherford H & Needham A 2010. The Prehistory of Compassion. Blurb, 106 pp. https://www.blurb.com/b/1628917-the-prehistory-of-compassion
Spikins P, Needham A, Tilley L & Hitchens G 2018. Calculated or caring? Neanderthal healthcare in social context. World Archaeology 50, 384–403. DOI: https://doi.org/10.1080/00438243.2018.1433060
Starr M 2024. Humans And Neanderthals Had a Longer, More Intertwined Relationship Than We Thought. ScienceAlert July 12, 2024. https://www.sciencealert.com/humans-and-neanderthals-had-a-longer-more-intertwined-relationship-than-we-thought
Stringer C & Crété L 2022. Mapping Interactions of H. neanderthalensis and Homo sapiens from the Fossil and Genetic Records. PaleoAnthropology 2, 401–412. DOI: https://doi.org/10.48738/2022.iss2.130
Thorpe N 2016. The Palaeolithic Compassion debate – Alternative Projections of Modern-Day Disability into the Distant Past. Chapter 6, pp. 93–110 in: Powell L, Southwell-Wright W & Gowland R (eds). Care in the Past: Archaeological and Interdisciplinary Perspectives. Oxbow Books, Oxford (UK), 208 pp. https://www.jstor.org/stable/j.ctt1kw290q.11
Tilley L 2015. Setting the Scene for a Bioarchaeology of Care. pp. 13–64 in: Theory and Practice in the Bioarchaeology of Care. Springer, Cham, xvii+319 pp. DOI: https://doi.org/10.1007/978-3-319-18860-7_2
Tilley L 2022. Disability and Care in the Bioarchaeological Record. Meeting the Challenges of Being Human. pp. 457–481 in: Grauer AL (ed.). The Routledge Handbook of Paleopathology. Routledge, London (UK), 692 pp. https://www.taylorfrancis.com/chapters/edit/10.4324/9781003130994-28/disability-care-bioarchaeological-record-lorna-tilley
Valença T & Falótico T 2023. Life and death of a disabled wild capuchin monkey infant. Primates 64, 207–213. DOI: https://doi.org/10.1007/s10329-023-01052-1
The Bishop's Mitre: a brief history.
Mitre, liturgical headdress worn by Roman Catholic bishops (including cardinals, archbishops, and popes) and abbots and some Anglican and Lutheran bishops. It has two shield-shaped stiffened halves that face the front and back. Two fringed streamers, known as lappets, hang from the back. It developed from the papal tiara and came into use in the 11th century. The mitre is worn over a zucchetto, a silk or polyester skullcap. See also religious dress.
Three types of mitres are worn in the Roman Catholic Church. The simplex is made of undecorated white linen or silk and is worn at funerals, on Good Friday, and for some other services, such as Candlemas. The auriphrygiata is made of plain gold cloth or white silk with gold or silver embroidered bands and is worn during penitential seasons (Advent and Lent) and at some other times. The pretiosa is decorated with precious stones and gold and worn on Sundays and feast days, as well as for ceremonies such as the election of a pope, the consecration of a bishop, or the canonization of a saint.
The Greek mitra worn by bishops and some Russian clergy in the Eastern churches is similar to a closed crown with a cross on top.
Yet more on why there is truly no place like home.
Study: Geological Habitability Parameters Imply Earth is Special and Advanced Life Extremely Rare
Looking forward to the August 27 release of the new edition of The Privileged Planet, which you can pre-order now, we’ve been considering issues of habitability — on Mars (here and here), and on the moons Enceladus and Titan. Now comes a new paper in Scientific Reports, “The importance of continents, oceans and plate tectonics for the evolution of complex life: implications for finding extraterrestrial civilizations.” It argues that extraterrestrial “advanced communicative civilizations” (or ACCs) must be extremely rare in the universe. Their logic is simple: ACCs would require planets with continents, oceans, and plate tectonics, but these major geological features of Earth are likely to be very rare elsewhere. If these features are required for ACCs, and if they are rare, then such advanced civilizations must also be very rare.
An excellent article at Nautilus, “The Odds That Aliens Exist Just Got Worse,” explains the paper’s basic findings: “The likelihood that other technologically sophisticated societies exist is smaller than previously thought, because basic amenities we take for granted on Earth — continents, oceans, and plate tectonics — are cosmically rare.” But if we take these findings out of the context of current obsessions over aliens, then the implication, of course, is simply that Earth is very privileged because the presence of continents, oceans, and plate tectonics on our planet is extremely rare.
Unknowns of the Drake Equation
As a geologist, what I find most fascinating about this Scientific Reports article is that it adds new geological factors to the Drake equation. That is the famous equation that is used to roughly calculate the number of technologically advanced extraterrestrial civilizations in our galaxy. The Nautilus article notes that the values of some factors in the classical formulation of the Drake equation are very difficult to estimate, particularly:
the fraction of potentially habitable planets on which life likely has emerged (a variable that’s completely unconstrained, since only one case — ours — is known); the fraction of those planets on which intelligent life has developed (a criterion that often elicits dark humor about whether human life qualifies); the fraction of that fraction that have sent signals into deep space (again, just one known example, out-going calls only); and the length of time those civilizations have been sending such signals (to be determined).
Some argue that even the low ends of reasonable estimated ranges for these factors imply that ET life should be sending telecommunications to us Earthlings. So why aren’t we getting any signals? This absence of ET life communicating with us is known as the “Fermi Paradox.”
How to Resolve the Fermi Paradox?
There are many possible ways to understand why we aren’t hearing from ET life — not the least of which is that, as the best evidence suggests, life is extremely unlikely to arise via natural chemical means. But the Nautilus article explains that the study tried to resolve the paradox by arguing that very few planets have the requisite geological factors needed for advanced life to arise:
Bringing a geologic perspective to the problem, Stern and Gerya propose to resolve the paradox by adding two more factors to the already unwieldy Drake equation: the fraction of habitable planets with distinct continents and oceans; and the fraction of those planets with a plate tectonic system that has operated for at least 500 million years. The values of these terms are very small, they argue, because the development of distinct landmasses and water bodies, and the tectonic habit of crustal recycling — characteristics of Earth that we take for granted — are unlikely outcomes in the evolution of rocky planets.
With these new factors, the number of advanced civilizations in our galaxy that might communicate with us falls to … almost zero.
The technical paper explains that a planet where ACCs evolve requires ocean basins, continental dry land, and plate tectonics: “Although primitive life must evolve in the sea, advanced communicative civilizations must evolve on dry land.” In light of these requirements, it proposes geological terms for resolving the Fermi Paradox:
We resolve the Fermi Paradox (1) by adding two additional terms to the Drake Equation: foc (the fraction of habitable exoplanets with significant continents and oceans) and fpt (the fraction of habitable exoplanets with significant continents and oceans that have had plate tectonics operating for at least 0.5 Ga); and (2) by demonstrating that the product of foc and fpt is very small (< 0.00003–0.002).
Note the value at the end: “< 0.00003–0.002.” If you add a factor with that value to the Drake equation, it suggests that ACC life elsewhere in the galaxy is extremely rare — if it exists at all.
Plate Tectonics Necessary for Life
There are multiple reasons why plate tectonics is necessary for life — something I spoke about in my talk at Discovery Institute’s 2022 Dallas Conference on Science and Faith.
Thus, I wholeheartedly agree with the Nautilus article when it states:
Most geologists will agree with Stern’s and Gerya’s argument that plate tectonics should be included as a criterion for long-term planetary habitability. Earth’s tectonic system allows the planet’s atmosphere and hydrosphere to remain in communication with its interior, in a remarkable, self-perpetuating cycle. Subducted ocean crust — seafloor that slips down into Earth’s interior — carries water back into the mantle, and at shallow depths, this water lowers the melting temperature of mantle rock, giving rise to unusual magmas that create the continental crust — what we surface dwellers live on — which is rich in rare elements, like phosphorus, that are critical to life.
At greater depths, subducted water acts to decrease the viscosity of the mantle, allowing it to churn, or convect, more vigorously — which in turn drives plate motion. When the Earth’s mantle exports heat via convection, it encourages the liquid iron outer core to convect as well, and this generates Earth’s protective magnetic field, which shields the surface environment from harmful cosmic radiation. Without plate tectonics, continents would quickly be eroded to sea level. But tectonic collisions continuously rejuvenate Earth’s topography, providing rivers with more energy to transport nutrient-rich sediments to shallow marine environments. In other words, plate tectonics is entangled with all the phenomena that support life on Earth.
So plate tectonics is vital for generating our magnetic field (necessary for life), maintaining the presence of life-necessary elements in the oceans, and creating both continents and oceans (which, if you haven’t noticed, are also vital for advanced life). This is all very reasonable, as is the study’s conclusion that plate tectonics is probably very rare on planets in the universe.
One reason for this is that all of the other rocky planets in our solar system have something called “stagnant lid” tectonics. That’s where the lithosphere of a planet is composed of a single plate and only vertical tectonic movement occurs due to upwelling from the mantle, but not horizontal plate movement. Earth is the only known planet to have horizontal plate tectonics movement, suggesting it is rare:
How Old Is Plate Tectonics on Earth?
One thing that is likely to get some pushback is the study’s claim that modern-style plate tectonics on Earth did not commence until the Neoproterozoic, which lasted from about 1 billion years ago until the beginning of the Cambrian period (about 540 million years ago). Many geologists, including many who work in paleomagnetism (the field of my PhD research), would argue that plate tectonics began very early in Earth’s history. That’s because we see evidence of continents on the move going all the way back into the Archean. But this controversy should not affect the paper’s basic claim. Here’s why:
The value of their fpt factor, added to the Drake equation, assumes that plate tectonics has only been operating on Earth for about 0.5 Ga (Ga = gigaannum, or a billion years). If plate tectonics has been operating for longer than that, it would presumably make Earth even more special, because plate tectonics would be longer lasting. In other words, in estimating the specialness of Earth, the paper’s calculations are conservative. In any case, however long plate tectonics has been operating on our planet, it seems that any other planets with plate tectonics, continents, and oceans are rare, and very special indeed.
Our Lord and Savior is a biblicist.
John ch.17:17KJV"Sanctify them through thy truth: thy word is truth."
John ch.5:39KJV"Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."
John Ch.5:45KJV"“But do not think I will accuse you before the Father. Your accuser is Moses, on whom your hopes are set."
Luke Ch.16:29-31KJV"Abraham saith unto him, They have Moses and the prophets; let them hear them.And he said, Nay, father Abraham: but if one went unto them from the dead, they will repent. 31And he said unto him, If they hear not Moses and the prophets, neither will they be persuaded, though one rose from the dead."
Luke Ch.24:32KJV"And they said one to another, Did not our heart burn within us, while he talked with us by the way, and while he opened to us the scriptures?"
The true Spirit of JEHOVAH causes reverence for and clear understanding of JEHOVAH'S Word the Holy Bible,any Spirit exalting tradition over JEHOVAH'S Word or promoting irrational exegesis of same is of a different source.
Thursday, 15 August 2024
Yet another neoDarwinian looking for frenemies?
James Shapiro: Intelligent Design “Has a Valid Point with Regard to the … Limits of Neo-Darwinism”
Earlier this year, the National Association of Scholars recently published an interesting issue of their journal Academic Questions. It’s on a special theme, “The State of Evolution,” and it includes many articles that are worth reading. One article, by University of Chicago biologist James Shapiro, is titled, “Evolution Is Neither Random Accidents nor Divine Intervention: Biological Action Changes Genomes.” Shapiro provides a very nice review of various functions that have been discovered for transposable elements — a type of repetitive DNA that was once labeled “junk,” but which we now know is “needed for various aspects of genome function.” He writes:
[R]epetitive DNA was labelled as “junk DNA,” “selfish DNA,” or “selfish genetic elements.” Richard Dawkins famously erected a widely popular philosophy of evolution on the basis of “The Selfish Gene” (1976).
Today, we recognize that most of this repetitive DNA is made up of transposable elements and other repeats needed for various aspects of genome function, especially developmental regulatory networks controlling cellular differentiation. The repeats help guide the origin of cell lines that comprise distinctive tissues, say bone tissue versus nervous tissue. Both have the same DNA, yet each cell type expresses the genome in distinctive ways controlled by different DNA repeats.
A Curious Comment
I highly recommend the paper. It also includes a curious comment about intelligent design:
Support for evolution guided by divine intervention has a toehold in the quasi-scientific Intelligent Design (ID) movement, initiated by Michael Behe (“Darwin’s Black Box: The Biochemical Challenge to Evolution,” 1996) and carried on by members of the Discovery Institute and other creationist think tanks. The basic argument that ID theorists make is that natural selection of random hereditary changes cannot produce genomes capable of expressing all the intricate networked adaptations modern molecular biology has revealed to operate in living organisms. This conundrum is, in Behe’s words, “irreducible complexity.” Hence, the ID theorists posit a need for divine intervention.
The ID argument has a valid point with regard to the explanatory limits of neo-Darwinism, still widely regarded as the only legitimate scientific explanation of evolution. ID falls down by assuming (as do mainstream evolutionists) that genome change occurs from outside the boundaries of life itself. Within the scientific community, there is agreement that the hereditary variation necessary for evolutionary change occurs by natural means. But significant difference exists between scientists about what constitutes “natural means.”
Shapiro is a great biologist who has offered many keen insights into the nature of genomic functioning. He’s clearly not an ID proponent and that is fine. I would disagree with his characterization of ID as a negative argument against evolution in favor of “divine intervention.”
The Struggles of Neo-Darwinism
But he’s absolutely correct to note that neo-Darwinism struggles to account for the “intricate networked adaptations modern molecular biology has revealed to operate in living organisms.” And I appreciate his recognition that ID got this one right. Shapiro thinks that natural genetic engineering can account for many of this intricate complexity — and we in the ID movement are interested in seeing how far these mechanisms of pre-programmed evolution can take us.
For my part, I think they might be useful for fine-tuning pre-existing functions — and may be involved in what Emily Reeves recently wrote about as “continuous environmental tracking.” But I’m skeptical that Dr. Shapiro’s model can account for much of the basic complexity of life. For the moment, I’m content to be grateful to him as a non-ID scientist who recognizes something ID has gotten right.
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.
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