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Tuesday, 6 December 2022

On Darwinism's failure as a predictive model VI

 By Cornelius G Hunter 

Histones are proteins which serve as the hubs about which DNA is wrapped. They are highly similar across vastly different species which means they must have evolved early in evolutionary history. As one textbook explains, “The amino acid sequences of four histones are remarkably similar among distantly related species. … The similarity in sequence among histones from all eukaryotes indicates that they fold into very similar three-dimensional conformations, which were optimized for histone function early in evolution in a common ancestor of all modern eukaryotes.” (Lodish et. al., Section 9.5) And this high similarity among the histones also means they must not tolerate change very well, as another textbook explains: “Changes in amino acid sequence are evidently much more harmful for some proteins than for others. … virtually all amino acid changes are harmful in histone H4. We assume that individuals who carried such harmful mutations have been eliminated from the population by natural selection.” (Alberts et. al. 1994, 243)


So the evolutionary prediction is that in these histone proteins practically all changes are deleterious: “As might be expected from their fundamental role in DNA packaging, the histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and a cow differ at only at 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell.” (Alberts et. al. 2002, Chapter 4) 

This prediction has also been given in popular presentations of the theory: “Virtually all mutations impair histone’s function, so almost none get through the filter of natural selection. The 103 amino acids in this protein are identical for nearly all plants and animals.” (Molecular Clocks: Proteins That Evolve at Different Rates)


But this prediction has turned out to be false. An early study suggested that one of the histone proteins could well tolerate many changes. (Agarwal and Behe) And later studies confirmed and expanded this finding: “despite the extremely well conserved nature of histone residues throughout different organisms, only a few mutations on the individual residues (including nonmodifiable sites) bring about prominent phenotypic defects.” (Kim et. al.)


Similarly another paper documented these contradictory results: “It is remarkable how many residues in these highly conserved proteins can be mutated and retain basic nucleosomal function. … The high level of sequence conservation of histone proteins across phyla suggests a fitness advantage of these particular amino acid sequences during evolution. Yet comprehensive analysis indicates that many histone mutations have no recognized phenotype.” (Dai et. al.) In fact, even more surprising, many mutations actually raised the fitness level. (Dai et. al.) 

References 

Agarwal, S., M. Behe. 1996. “Non-conservative mutations are well tolerated in the globular region of yeast histone H4.” J Molecular Biology 255:401-411.


Alberts, Bruce., D. Bray, J. Lewis, M. Raff, K. Roberts, J. Watson. 1994. Molecular Biology of the Cell. 3d ed. New York: Garland Publishing.


Alberts, Bruce., A. Johnson, J. Lewis, et. al. 2002. Molecular Biology of the Cell. 4th ed. New York: Garland Publishing. http://www.ncbi.nlm.nih.gov/books/NBK26834/


Dai, J., E. Hyland, D. Yuan, H. Huang, J. Bader, J. Boeke. 2008. “Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.” Cell 134:1066-1078.


Kim, J., J. Hsu, M. Smith, C. Allis. 2012. “Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast.” Proceedings of the National Academy of Sciences 109:5779-5784.


Lodish H., A. Berk, S. Zipursky, et. al. 2000. Molecular Cell Biology. 4th ed. New York: W. H. Freeman. http://www.ncbi.nlm.nih.gov/books/NBK21500/


“Molecular Clocks: Proteins That Evolve at Different Rates.” 2001. WGBH Educational Foundation and Clear Blue Sky Productions.

The fossil record goes awol again re:Darwinism.

Springtails: Wingless Arthropods that Can Fly 

David Coppedge

If you’ve hiked along streams and lakes, you may have noticed tiny bugs moving about on the water, appearing to pop into the air like popcorn. They were probably springtails: tiny non-insect hexapods without wings. Evolutionary biologists used to think that hexapods like this evolved into insects when they first earned their wings, but news from Stanford points out several problems with that idea. The fossil record shows a “Hexapod Gap”: 

“There’s been quite a bit of mystery around how insects first arose, because for many millions of years you had nothing, and then just all of a sudden an explosion of insects,” said study first author Sandra Schachat, a graduate student at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth).


Many ideas have been proposed to explain this curious lacuna in the insect fossil record, which scientists have dubbed the Hexapod Gap. 

Unfortunately for Darwin, the two leading theories to explain the gap can be ruled out; “No Excuses,” the news items says in a subtitle, silently agreeing that the insect explosion mentioned in the Science uprising episode about fossils is real:

The only way to preserve Darwinism is with a just-so story. 

As part of the new study, the team reexamined the ancient insect fossil record and found no direct evidence for wings before or during the Hexapod Gap. But as soon as wings appear 325 million years ago, insect fossils become far more abundant and diverse.


“The fossil record looks just how you would expect if insects were rare until they evolved wings, at which point they very rapidly increased in diversity and abundance,” Payne said. 

So Much for Darwin; Let’s Try Design Thinking 

A closer look at springtails shows admirable design. Six scientists from South Korea and from Georgia Tech investigated these little gymnasts. Publishing in PNAS, Victor M. Ortega-Jimenez and his team wrote about “Directional takeoff, aerial righting, and adhesion landing of semiaquatic springtails.” After refuting some myths about them, the scientists expressed amazement at their acrobatic abilities. 

Springtails are the largest group of noninsect hexapods renowned for their unique and enigmatic appendices for jumping (furcula) and adhesion (collophore). However, it has been erroneously assumed that they are unable to control their explosive takeoff, mid-air spinning, and landing. We discover that semiaquatic springtails can indeed control all three phases of jumping by adjusting their body posture and taking advantage of their appendages. They adjust the body angle and actuation speed of their leaping organ during takeoff, change their body posture in midair, and exploit the hydrophilic property of their ventral adhesive tube. The combination of these strategies allows springtails to achieve locomotion control, stability, and maneuverability, which can inform the design of small bio-inspired robots with controlled landing. 

To appreciate what they found, one must watch the slow-motion videos from the project, which are embedded in the paper. The graceful performances, with high jumps, flips, spins, and explosive horizontal dashes, are stunning enough for Olympic “short performances” in tumbling. The hexapods perform their stunts in tuck, pike, and full layout positions. And then, being able to “stick” the landing is a goal of every gymnast. The little bugs “perform directional jumps, rapid aerial righting, and near-perfect landing on the water surface,” nailing the landing 87 percent of the time after rotating so fast the action would look like a blur if not slowed down to 10,000 frames per second. This silent video really needs music!


Imitation is the sincerest form of flattery. After watching the performance, the judges tried to copy the design: 

We validated the springtail biophysical principles in a bioinspired jumping robot that reduces in-flight rotation and lands upright ~75% of the time. Thus, contrary to common belief, these wingless hexapods can jump, skydive, and land with outstanding control that can be fundamental for survival. 

Who Needs Wings? 

Springtails are among the smallest of arthropods, measuring 0.2 to 10 mm in length. They may seem deprived compared to their winged insect neighbors, but their physical prowess exceeds their humble appearance. The South African Biodiversity Institute tells us that they live on every continent, “even in the most inhospitable environments such as Antarctica and the Namib desert.” Their specialized exoskeleton lets them move easily on water: “Most interestingly, their skin has comb-like hexagonal or rhombic granules that are water repellent and self-cleaning.” 


Classified in phylum Arthropoda, class Entognatha, subclass Collembola, springtails are not harmful to humans unless they pop into your house by the hundreds for a visit and become a nuisance. They live on algae, fungi, and detritus, and rarely harm plants. And yes, these tiny gymnasts contain all the necessary equipment for sensation, digestion, movement, circulation, mating, sex, and communication. Like everything else, they run on ATP, with complex specified information encoded in DNA. All the respiratory and epigenetic systems that I discussed in my recent article about mitochondria are at work in their tiny bodies.

Anatomy and Physiology for Gymnastics 

The name “springtail” comes from the furcula under the abdomen, a forked, spring-like appendage powerful enough to launch them several meters into the air. Some of the 650 species of springtails that live in soil lack this organ. Another distinctive organ of springtails is the collophore, a tube-like structure under the abdomen. The PNAS paper tells how this organ plays a key role in the little bugs’ acrobatics: 

We discover that semiaquatic springtails, Isotomurus retardatus, can perform directional jumps, rapid aerial righting, and near-perfect landing on the water surface. They achieve these locomotive controls by adjusting their body attitude and impulse during takeoff, deforming their body in midair, and exploiting the hydrophilicity of their ventral tube, known as the collophore. 

Researchers proved that this organ prevents bouncing on landing. The collophore picks up a drop of water at launch. On landing, the droplet grips the surface by water cohesion, providing a cushioned impact and adhesion so that the bug doesn’t bounce. 

Experiments and mathematical modeling indicate that directional-impulse control during takeoff is driven by the collophore’s adhesion force, the body angle, and the stroke duration produced by their jumping organ, the furcula. In midair, springtails curve their bodies to form a U-shape pose, which leverages aerodynamic forces to right themselves in less than ~20 ms, the fastest ever measured in animals. A stable equilibrium is facilitated by the water adhered to the collophore. 

Another trick in the springtail’s repertoire is the rapid skip. Springtails can scoot across the water horizontally at amazing speeds, using both the furcula and collophore. 

In a few extreme cases, we even observed individuals locomote on the water surface without detaching the collophore from the surface. These springtails were able to skip on the water surface, frequently actuating their furcula. They reached traveling speeds of up to 28 cm/s (~280 bodies per s) …We observed that springtails moving horizontally on the water use their legs to adjust their yaw direction before each leaping. 

Watch and Wonder 

A truly astonishing set of springtail jumps was filmed by Dr. Adrian Smith at the North Carolina Museum of Natural Sciences. His YouTube video on the Ant Lab channel shows what the tiny springtails look like close up. He shows them leaping more than 86 times their body height into the air and rotating in 14 somersaults or more at 290 flips per second! The final clips, filmed at 73,510 frames per second, show how the furcula works: it slaps the surface, bends at a knee-like joint, and then arcs backward under the body, eventually folding back into position in midair. 

For an encore, Smith posted another YouTube video

He collected springtails in his backyard and filmed them at double the previous speed: 150,000 fps. One member of an elongated species took 0.0048 seconds to take off, accelerating at 80 m/s2 or 8 G. That was only the silver medalist! A globular species took off in a third of that time (0.0015s), accelerating at 798 m/s2 or 81 G, ten times the other one’s g-force! It’s a marvel that the head doesn’t separate and fly off under that kind of physical stress. And yet these tiny creatures jump like that all day long, every day.


Awe and Intelligent Design

People travel the world to watch the Olympic Games every four years. The gymnastics competitions are among the most popular. Without diminishing the human skill, strength, and artistry in those events, here we have seen wonders in a scientist’s backyard of equal magnificence that most of us pass by unaware. Most scientists are trained to have a keener sense of awareness of the world around them. They like to observe phenomena in detail to understand how they work. None of these scientists needed Darwinism in their study. The expectation of a functional design capable of explaining the feat sufficed to motivate the research. 


Isn’t that one of the key benefits of design thinking for science? Curiosity leads to attention, attention to observation, observation to research, research to innovation to improve observation, innovation to understanding, and understanding to imitation. Throughout that “evolution” — defined in its etymological sense of unfolding, from the Latin evolvere — intelligent design was implicitly present whether the scientist was aware of it or not.


Something else builds on understanding: awe. Many scientists testify that awe of nature led them to seek a career in science. Design science, I believe, yields a cornucopia of awe for which we can be thankful.