Selection, the Principle of Evolution

In The Origin of Species, Charles Darwin introduced the principle of selection as the agent driving evolution. In the words of Niles Eldredge, the curator of the American Museum of Natural History –

“When [Darwin] formulated the principle of natural selection, he had discovered the central process of evolution.”

Interestingly, English zoologist and chemist Edward Blyth introduced the phrase “natural process of selection” twenty years earlier. In the first chapter of The Origin of Species, Darwin credits Blyth, noting –

“Mr. Blyth, whose opinion, from his large and varied stores of knowledge, I should value more than that of almost anyone.”

Niles Eldredge (pictured right) iconized the V.I.S.T.A. acronym for studying natural selection in Darwin: Discovering the Tree of Life. The five principles of natural selection include variation, inheritance, selection, time, and adaptation.

Selection acts to bring things together, like in the water flea (pictured above). It acts to bring things together, like in the water flea. While selection is Darwin’s most critical principle, it is also the most controversial of the five.

Natural Selection

The title of Darwin’s historic book summarizes how the origin of Earth’s biosphere happened – “by means of natural selection”

“On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life”

The book was an instant bestseller, selling all 1,250 printed copies on the first day. However, critics quickly centered on challenging his similar but novel theory.

Definitions

Interestingly, in what was known as the progressive writing style at the time, Darwin did not include a definition of his two keywords, natural or selection, or the phrase natural selection. Only the 6^th Edition included a Glossary written by W.S. Dallas, not Darwin.

However, based on Darwin’s explanations and inferences, “natural” means autonomy, free of intervention, and “selection” means to choose. Darwin’s explanations were often vague, driven more by speculations than scientific evidence. For example, Darwin explains –

“In order to make it clear how, as I believe, natural selection acts, I must beg permission to give one or two imaginary illustrations.”

This progressive writing style was popular during the Age of Enlightenment. Vagueness allowed readers the license to speculate on their own, a style successfully used by his grandfather, Erasmus Darwin. However, addressing conflicted explanations and criticisms from friends and foes prompted the rewriting of five significant revisions of his bestseller.

Between the 5^th and the 6^th Editions alone, sixty-three sentences were eliminated, 1,699 sentences were re-written, and 517 sentences were added. “Natural selection” appears 315 times in the first Edition and 405 times in the last. Eventually, Darwin acknowledged in The Origin of Species –

“Natural selection… is by far the most serious special difficulty which my theory has encountered.”

Selective Breeding

The title of Chapter I in The Origin of Species is “Variation Under Domestication.” Natural selection, Darwin argued, is analogous to domestic breeding practices of improving their herds.

As the principle of selection drives preferred varieties in domestic livestock, this principle likewise drives improvements in nature, Darwin argues –

“Can the principle of selection, which we have seen is so potent in the hands of man, apply under nature? I think we shall see that it can act most efficiently.”

Selection drives the changes –

“Over all these causes of Change, I am convinced that the accumulative action of Selection, whether applied methodically and more quickly, or unconsciously and more slowly, but more efficiently, is by far the predominant Power.”

Selection acts by choosing between available variations –

“The great power of this principle of selection is not hypothetical. It is certain that several of our eminent breeders have, even within a single lifetime, modified to a large extent their breeds of cattle and sheep.”

While the natural selection and selective breeding analogy once played an essential conceptual role, it has since emerged as a theoretical “origin of species” enigma.

“How Selection Acts” Critique

In an article published by Revue Horticole in 1852, French naturalist Charles Victor Naudin (pictured right) predated Darwin’s version of natural selection. Darwin critiqued Naudin’s theory in The Origin of Species beginning with the 3^rd Edition, noting –

“In 1852, M. Naudin, a distinguished botanist, expressly stated, in an admirable paper on the origin of species… his belief that species are formed in an analogous manner as varieties are under cultivation; and the latter process he attributes to man’s power of selection. But he does not show how selection acts under nature.” 6^th Edition.

With the phrase “show how selection acts under nature,” Darwin set the bar. Although not addressing the “how selection” issue, Darwin approached the “why issue” by introducing the concept of sexual selection.

Sexual Selection

Sexual selection is Darwin’s (pictured left) explanation to account for showy mating traits. This interest nearly matched his fascination with natural selection. Written in his “Old and Useless Notes“ in 1838, Darwin recorded searching for an answer to the question –

“How does Hen determine most beautiful cock, which best singer?”

Natural selection equips the struggle for existence. Sexual selection equips males and females with secondary sexual characters for intrasexual reproduction competition, Darwin explains –

“This leads me to say a few words on what I have called Sexual Selection. This form of selection depends, not on a struggle for existence in relation to other organic beings or to external conditions, but on a struggle between the individuals of one sex, generally the males, for the possession of the other sex. The result is not death to the unsuccessful competitor, but few or no offspring.”

The term “sexual selection” appears twenty-one times in The Origin of Species. Describing sexual selection further, Darwin notes –

“Sexual selection has given the most brilliant colours, elegant patterns, and other ornaments to the males, and sometimes to both sexes of many birds, butterflies, and other animals (male/female right).”

The same term appears 104 times in The Descent of Man, published in 1871, Darwin concedes –

“The precise manner in which sexual selection acts is to a certain extent uncertain.”

Sexual selection may explain “why” but does not reach the “how” bar.

Modern Synthesis Theory of Evolution

Early in the twentieth century, the emergence of the modern synthesis theory of evolution seemingly resolved Darwin’s red line. This newly synthesized theory integrated Darwin’s natural selection, Gregor Mendel’s genetic laws of inheritance, and R.A. Fisher’s (pictured left) population model.

The discovery of the DNA structure early in the 1950s opened a new avenue to study Mendel’s inheritance laws. Since then, a gene-centric approach has primarily driven the field of biological evolution.

The prospect of developing a cohesive gene-centric theory of evolution prompted Theodosius Dobzhansky,(pictured right) geneticist and biologist, to declare in 1973 –

“Nothing in biology makes sense except in the light of evolution.”

An organism’s genotype, governed by a pair of alleles, contributes to its physical expression, known as phenotype. Alleles are specific sequences of nucleotides. The pair, one from each parent in diploid organisms, are expressed and interact to produce its physical characteristics.

In evolution, selection combines things by choosing between accepting or eliminating inheritable molecular variations. Reaching the “show how selection acts” bar seemed increasingly probable.

Types of Selection

The race to discover how selection acts to change populations phylogenetically was on. Investigators identified three main types: directional, disruptive, and stabilizing.

Directional selection favors one extreme phenotype over other extreme and moderate types. Domestic breeding applies is directional.
Disruptive and diversifying selection favor extreme phenotypes over intermediate types. Divergent drives populations towards speciation.
Stabilizing selection favors intermediate phenotypes over extreme types, the opposite of disruptive. Stabilizing is conservational.

Balancing, fluctuating, and negative, also known as purifying selection, are minor terms. However, the practical application of categorizing selection processes has been inconsistent.

Darwin’s finch beaks and Kettlewell’s peppered moths are featured as examples of directional selection by some and disruptive selection by others. Home sapiens have been variably classified as examples of stabilizing and directional selection.

However, none of the selection types explain how chromosomal alleles are inserted, eliminated, or exchanged.

Live Study Models

The Galapagos finches, peppered moths, and the Giraffes’ long necks are classic examples of Darwin’s theory. However, in the search to explain “how selection acts under nature,” studying more rapidly reproducing populations allows investigators to observe how it works scientifically.

The co-emergence of genomics and the modern synthesis theory launched an unprecedented opportunity to study natural selection in real-time. By the late twentieth century, microbes emerged as one of the most valuable models for studying how it acts in nature.

Microbes

Escherichia coli (E. coli), a pathogenic bacterium, is a model organism for studying how selection acts. Its generation time is about 20 minutes, meaning the population doubles every 20 minutes. Rapidly reproducing populations produce a treasure trove of data for scientists to study.

Biologist Richard Lenski at Michigan State University launched his now legendary experiment in his laboratory early in 1988 with 12 laboratory flasks (pictured left) seeded with the genetically identical Escherichia coli (E. coli).

Decades later, writing for Science Alert, Fiona MacDonald in 2017, puts the comparison between Lenski’s bacteria test and human evolution into context, noting –

“Scientists have spent the past 30 years carefully tracking evolution across more than 68,000 generations of E. coli bacteria – the equivalent of more than 1 million years of human evolution.”

Varying ecosystem changes over the decades systematically challenged Lenski’s (pictured right) 12 lineages of bacteria. With each generation sampled and preserved, Lenski and his colleagues documented a vast collection of phenotypic and genotypic changes in the evolving populations throughout the experiments.

Over the first 20,000 generations, the bacteria in each flask generated hundreds of millions of random mutations. However, each population reported 10 to 20 fixed mutations.

Alejandro Couce (pictured left) and Lenski published their extended analysis at the 50,000 generation point in the journal Science this year (2024). Entitled “Changing fitness effects of mutations through long-term bacterial evolution,” the journal’s editor noted –

“The numbers of beneficial mutations rapidly tailed off during long-term passage, with parallel changes in fitness cost and gene essentiality occurring across the lineages. The authors found nonessential genes that became essential and essential genes that became nonessential in all lineages.”

After starting with E. coli in 1988, all flasks continued to reproduce only E. coli. Notably, after decades of observing genetic mutations, an explanation to describe “how selection acts under nature” to drive evolution has yet to emerge.

In science, when one door closes, another door opens.

The Water Flea

Daphnia pulex (D. pulex), a tiny planktonic crustacean water flea, fascinates biologists due to its adaptivity, including predation. It is the most common species of water flea found throughout the Americas, Europe, and Australia.

D, pulex (pictured left) is a vital food source for fish and checking algae growth in diverse and changing ecosystems. As the first crustaceans to have their genomes sequenced, they emerged as a model for studying the interplay between selection, genotype, and phenotype—natural selection in action.

The capacity to change between phenotypes within a generation is known as phenotypic plasticity. The intragenerational cycling between asexual and sexual reproduction (parthenogenesis) in D. pulex and neck morphology are examples of phenotypic plasticity.

D. pulex populations build defenses by morphing their dorsal necks (pictured right) into “neck teeth” as predators enter their biosphere. Daphnia makes easy prey for both vertebrate and invertebrate predators. Observing these defensive phylogenetic changes offers a live model for studying “how selection acts” in nature.

“Neck Teeth” Approach

D. pulex (pictured left) develops a strange morphological protective defense against one of its most troubling predators: fish and the grassworm Chaoborus larvae. Developing on-demand neck teeth (NK) from its dorsal fin is one of the water fleas’ most interesting types of anti-predator responses.

Morphological changes begin once the water flea detects the chemical clues released by the Chaoborus larvae.

Dorthe Becker, a professor at the University of Sheffield, GB, recently completed a study of the phylogenetic plasticity of the water flea’s anti-predator defenses. Their report, “Adaptive phenotypic plasticity is under stabilizing selection in Daphnia,” was published in the journal Nature Ecology and Evolution (2022) explain the motivation for the study –

“Little is known about the evolutionary forces that shape genetic variation of plasticity within populations.”

The study aimed to assess the type of selection, stabilizing or diversifying. While stabilizing is conservational, diversifying selection drives evolution. Becker (pictured right) notes –

“Here, we address this issue by assessing the evolutionary forces that shape genetic variation in antipredator developmental plasticity of Daphnia pulex.”

The title of the team’s 2022 report, “Adaptive phenotypic plasticity is under stabilizing selection in Daphnia,” summarizes their findings. Selection in the water flea drives conservation, not evolution.

Stabilizing selection plays an adaptive role in conserving the most common phenotype for future generations. The evidence, however, never showed “how selection acts under nature.”

As one approach closes, another approach opens.

Selection Coefficient Approach

Michael Lynch, director of the Biodesign Institute at Arizona State University, published their team’s 10-year water flea population-genomic survey. Their report, “The genome-wide signature of short-term temporal selection,” was published in Proceeds of the National Academy of Science (PNAC) in July 2024.

In the water fleas, Lynch found “little [genetic] evidence of positive covariance of selection across time.” The selection coefficient is a quantitative genotype description, a quantitative estimate of diversity. Lynch concludes –

“Most nucleotide sites experience fluctuating selection with mean selection coefficients near zero… These results raise challenges for the conventional interpretation of measures of nucleotide diversity and divergence as measures of random genetic drift and intensities of selection.”

The exchange of alleles over ten years did not produce changes in the flea’s genotype. With the findings, science writer Richard Harth (pictured right) took the high road in the article “Study challenges traditional views of evolution” –

“The study shows that evolution is more dynamic and complex than previously appreciated.”

Genesis

Ironically, in assessing the Genesis account of creation in The Origin of Species, Darwin concluded –

“On the ordinary view of the independent creation of each being, we can only say that so it is… but this is not a scientific explanation.”

Natural selection, a natural explanation for the origin of Earth’s biosphere, is beyond the reach of scientific validation—the Emperor of Evolution has no clothes.

As a French chemist and microbiologist renowned for his discoveries of the principles of vaccination, microbial fermentation, and pasteurization and regarded as a founder of the germ theory of diseases, Louis Pasteur declared –

“A bit of science distances one from God, but much science nears one to Him… The more I study nature, the more I stand amazed at the work of the Creator.”

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