Richard William Nelson
[Originally published as the second part of Adaptation, Fifth Principle of Natural Selection The first section discusses the history of thinking about natural selection and its function up to the turn of the 20th Century.]
Two Types of Biological Evolution
In the early twentieth century, evolutionary scientists struggled with a seeming disconnect between adaptation and speciation. Yuri Filipchenko, a Russian entomologist, coined the terms “microevolution” and “macroevolution” in the book, Variabilität und Variation, published in 1927.
Filipchenko integrated Mendelian genetics into a view of biological evolution as two distinct processes. While supporting Darwin’s small-scale concept of adaptive microevolution, Filipchenko upended Darwin’s adaptive explanation for the origin of new species. In The Origin of Species, Darwin had asserted:
The theory of natural selection is grounded on the belief that each new variety, and ultimately each new species, is produced.
Filipchenko toppled Darwin’s concept of extending microevolution “ultimately” to drive the formation of new species, that is, the concept of macroevolution.
Filipchenko viewed microevolution and macroevolution as distinctly different mechanisms. While microevolution is a successive, genetically driven adaptive process, macroevolution is a non-successive, non-adaptive process of speciation.
As the founder of the USSR Academy of Sciences Institute of Genetics, Filipchenko influenced the emerging gene-centric concepts of macroevolution.
Theoretical Shift
As the theory of evolution drew increasing interest and scrutiny, evolutionary scientists’ focus on emerging genetic concepts escalated. And, while adaptive changes within populations proved measurable, scientific measures for the emergence of new species proved problematic.
To explain this difficulty, evolutionists increasingly envisioned evolutionary change as two distinct processes independent of successive adaptations.
Modern Synthesis Theory
A disciple of Filipchenko, Theodosius Dobzhansky, wrote the 1937 book, Genetics and the Origin of Species, which played a significant role in the emergence of the Modern Synthesis.
Dobzhansky’s radiation-induced fruit fly experiments reinforced the centrality of concepts of genetic variation in evolutionary biology. His words remain enshrined as a mosaic in the halls of biology at the University of Notre Dame”
Nothing makes sense in biology, except in the light of evolution.
In 1942, evolutionary biologist Julian Huxley introduced the term “Modern Synthesis” in his book, Evolution: The Modern Synthesis. The same year, Ernst Mayr published Systematics and the Origin of Species. Huxley sought to unify biology within an evolutionary framework, whereas Mayr focused on the evolutionary mechanisms of speciation.
In his publication, Mayr accomplished what Darwin did not: define the term “species.” Known as the Biological Species Concept (BSC), the definition was pivotal for advancing the emerging Modern Synthesis theory of evolution.
Defining species as “reproductive isolation” lineages capable of producing fertile offspring upended the practice of defining species by visible appearances. Mayr’s inheritance-dependent definition of adaptation separated adaptation from speciation, heightening the shift toward a gene-centric view of evolution.
However, studying the shift scientifically requires technical support.
Genomic Revolution
In the mid-twentieth century, biotechnology equipment continued to expand its capacity to explore the secret drivers of life. Emerging recombinant DNA technologies, which allow genes to be analyzed, cut, spliced, and examined, launched the Genomic Revolution. And, while the scientific evidence for adaptive-driven microevolution became well established, adaptive-driven macroevolution remained — and remains — unestablished at any level.
Adaptation Limits
In 1988, Richard Lenski launched the longest-running evolutionary experiment in the history of evolutionary science. The Genomic Revolution enabled Lenski to test key molecular assumptions in assessing the crucial link between microevolution and macroevolution.
Coined as the long-term evolution experiment (LTEE), Lenski’s experiment tested the scope of nature’s adaptation processes. Using the bacterium E. coli, the experiment has now been running continuously for more than three decades.
The U.S. National Science Foundation (NSF) has funded Lenski’s project from the outset. The experiment is testing adaptive changes in the 12 original bacterial populations by progressively varying environmental conditions.
Each day, the cell sizes, growth rates, colony morphologies, and genomic sequences are measured and documented. Samples from each population are then preserved for reference and further study.Escherichia coli
The experiment is designed to test and link Darwin’s concept of adaptation-related variations to the emergence of new species — the “origin of species.”
In Pursuit of How
Answering Darwin’s question of how new species emerge from adaptations has remained beyond the reach of science. The genomic revolution offers the tools to address Darwin’s lingering “how” question scientifically.
The problem is not the lack of new species to study. Over recent decades, the rate of new species discoveries has exploded, now averaging an estimated 10,000 per year. And, despite the estimated 3-100 million eukaryotic species currently living on Earth’s biosphere, the lack of species to study is not the problem, either.
The absence of empirical evidence for adaptation-driven speciation calls into question whether adaptations can, in fact, drive speciation. Lenski’s experiment tests whether Darwin’s theory of adaptation-to-divergence-to-speciation is “how” evolution works.
Over decades of experimentation, Lenski has observed thousands of adaptively driven novelties emerge. However, none of these changes have met Mayr’s species criteria.
Coupled with the absence of empirical macroevolutionary observations published in peer-reviewed journals, efforts to revise the Modern Synthesis became increasingly inevitable.
Beyond Molecular Adaptations
In July of 2008, philosopher Massimo Pigliucci and evolutionary biologist Gerd B. Müller hosted an invitation-only conference to address issues in the Modern Synthesis. Dubbed “The Altenberg 16” in recognition of its 16 attendees.
At the Konrad Lorenz Institute for Evolution (KLI) in Austria, conference attendees discussed extending the mechanisms of Modern Synthesis beyond adaptations. In anticipation of heated press coverage, the press was barred from the meeting.
A report from the conference was never published, and the events remained secret for two years. But then in 2010, they released a book, Evolution: The Extended Synthesis, discussing the event. The attendees’ aim, as explained in the preface, was to address Darwin’s infamous how question beyond the limits of Modern Synthesis, noting:
“This is a propitious time to engage the scientific community in a vast interdisciplinary effort to further our understanding of how life evolves. An extended evolutionary framework will be key for this endeavor.”
Pigliucci and Müller organized the papers from the attendees into these seven sections: Variation and Selection, Evolving Genomes, Inheritance and Replication, Evolutionary Developmental Biology, Macroevolution and Evolvability, and Philosophical Dimensions.
Adaptation’s Role
Notably, none of the sections focused on the role of adaptations. However, in the Philosophical Dimensions section, written by Werner Callebaut of KLI, it was concluded:
It should not be thought that the Darwinian Revolution is over.
The search to understand how nature produces species remained unknown at the time. Callebaut entitled his chapter, “The Dialects of Dis/Unity in the Evolutionary Synthesis and Its Extensions,” which opened with the following sentence:
“The thesis of my contribution is that the evolution of evolutionary thinking since the making of the Modern Synthesis has been characterized by simultaneous unifying and disunifying tendencies, with no end in sight.”
Contrary to Pigliucci and Müller’s goals, the development of an extended evolutionary framework never materialized. A consensus on the role of adaptations within the cohesive extended evolutionary synthesis has never developed to account for macroevolution.
The Royal Society Referendum
In 2016, the Royal Society issued a call to renew efforts to revisit extending the Modern Synthesis theory of evolution’s dominant paradigm, noting:
Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution, although the issues involved remain hotly contested.
The three-day event was titled, “New Trends in Evolutionary Biology: Biological, Philosophical, and Social Science Perspectives.” Several hundred scientists attended the meetings.
Epigenetics, embryological plasticity, and multi-level systems concepts were discussed as potential mechanisms for extending Modern Synthesis. However, the Society did not reach consensus on how to resolve the deadlock over the link between microevolution and macroevolution.
Consequently, the meeting underscored the lack of a scientifically valid framework in evolutionary biology to account for the “origin of species.” The role of adaptation as a driver of macroevolution seemed inevitable.
Interestingly, Richard Lenski was not a participant in the Altenberg or Royal Society meetings.
Decades of Experimental Evolution
Before these two referendum conferences, Lenski had published dozens of significant, ongoing results from the LTEE. The publications documented fitness trajectories, increases in cell size, evolution of mutation rates, parallel versus divergent outcomes, and genomic changes.
Because of their high reproductive rates relative to humans, microbes are ideal models for evolutionary studies. Evolution proceeds by generations rather than clock time; a decade of microbial adaptations corresponds to millions of years in humans.
As of 2025, Lenski’s experiment had studied over 80,000 generations of E. coli, equivalent to nearly 2 million years of human existence. The duration of Lenski’s adaptation experiment is unparalleled in the evolutionary sciences.
Lenski’s Findings
In his nearly 30 years of study, Lenski has documented an accumulation of a range of adaptive changes across the 12 E. coli populations. These adaptive changes include shifts in energy utilization from glucose to citrate, genetic mutations, and the emergence of novel traits.
Despite these changes, all 12 original E. coli lineages remained E. coli; no lineage met Mayr’s definition of a new species. Lenski’s observations remained consistent, beginning with his first publication in 1991, noting:
These results, taken as a whole, are consistent with theoretical expectations that do not invoke divergence (speciation).
Lenski’s LTEE experiment demonstrates that adaptations emerge within a species (microevolution) in association with shifting environmental contingencies. The universal finding of adaptation within each species functions seamlessly within each species inherent design.
Adaptation Limitations
Adaptation is a conservation process, rather than a creative engine. An accumulation of adaptations once thought to bridge the gap between microevolution and macroevolution has never been observed.
Adaptation is not scientifically validated as a mechanism for transforming a species into a new species, as Darwin once argued. Modern adaptation studies have upended assumptions that antimicrobial resistance is illustrative of how new species emerge.
Twenty-first-century adaptation studies have upended long-held assumptions about adaptive-driven macroevolution, including popular giraffe assumptions.
The Giraffe Lesson
Lamarck and Darwin assumed that long necks evolved to give giraffes a competitive advantage by allowing them to reach leaves on tall trees. However, neither had any empirical supportive observations.
During the dry season, biologist Robert Simmons of Uppsala University studied wild giraffes’ feeding in Africa through direct field observations. In “Winning by a Neck,” published by The American Naturalist. Simmons reported:
“We find that during the dry season (when feeding competition should be the most intense) giraffes generally feed on low shrubs, not tall trees… Each result suggests that long necks did not evolve specifically for feeding at higher levels… We thus find little critical support for the Darwinian feeding competition idea.”
Although Lamarck and Darwin had a logical argument, the scientific evidence undermined it.
Genesis
French chemist and microbiologist, Louis Pasteur, discoverer of the principles of vaccination, microbial fermentation, and pasteurization, encapsulates the challenges to understand nature:
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.
The emergence of new species through adaptation-driven macroevolutionary processes is not a scientifically valid theory.
Evolution beyond adaptation is a theory in crisis.
