Rethinking Evolution

The following sections are included:

• Dedication
• Preface
• Acknowledgments
• About the Author
• Contents
• How to Use Rethinking Evolution

The following section is included:

• A Natural Explanation for Adaptations

The concept of emergent evolutionary potential (EEP) combines scientific perspectives of emergence and potential in the context of biological evolution (BE).

Concrete examples of biological emergence go a long way towards explaining the sheer organizing power of molecular interactions within living cells. At a variety of levels of complexity, new opportunities arise from previous innovations—particularly when formerly nonexistent or separate entities are brought together in new contexts.

This new perspective updates evolutionary theory and helps to explain the origins of diverse adaptations—not only how it arises, but also how it is reproduced during development, in each generation and in every individual.

Dobzhansky’s defense of the “Modern Synthesis” stated that “nothing in biology makes sense except in the light of evolution”.

In the UES, we can say:

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

This emphasizes the importance of the stunning advances in laboratory technology that have revolutionized our understanding of the inner-workings and molecular interactions in living cells.

Charles Darwin’s and Gregor Mendel’s broad, early insights into Natural Selection and Mendelian Genetics were brilliant, yet incomplete generalizations that were limited by the limited knowledge-base and technology of the 19^th century.

Today, any Updated Evolutionary Synthesis (UES) that is suitable for the 21^st century must be grounded in our more detailed knowledge-base as well as the major conceptual advances that have been made.

The current explanation for complex biological organization links changes in the genome to the tools that generate structure and function in each generation.

This arises during the development of the individual and is manifested in the day-to-day functions made possible by molecular interactions within living cells.

Evolutionary innovations lay the groundwork for subsequent innovations. They often represent tools and reusable modules that can evolve in a variety of ways—in different lineages and in different ecological contexts.

Molecular interactions involving proteins carry out virtually every function in living cells. They also mediate interactions between cells during development and are responsible for the overall patterning of the body and complex organization of individuals of every species.

The misleading concept of “random mutations” from the “Modern Synthesis” became more concrete with the discovery of DNA and its subsequent characterization. “Random mutations” were now thought of in terms of discrete changes in DNA sequences that translate into changes in specific proteins.

We now know that proteins are not the only type of genetic information. Evolution also acts to create, modify, and reuse regulatory sequences of DNA. A variety of regulatory DNA sequences interact in complex ways to control the expression of specific proteins.

The Updated Evolutionary Synthesis should also include six additional concepts that transcend the misleading concept that mutations are “random”: (1) Various modular and reusable tools have evolved that facilitate and accelerate genome evolution. The genome represents a metaphorical scrapyard of reusable genetic information.

(2) Platforms that bring cellular entities together create new opportunities for higher-level organization to emerge; this is a source of Emergent Evolutionary Potential (EEP).

(3) The concept of phenotype should include a distinction that emphasizes the difference between Generative and Ecological Phenotypes. The former are often tools that act during development, while the latter refers to the structures and functions of the individual that have adapted to various niches (ways of life).

(4) Random and fortuitous variation generates a metaphorical “scrapyard” of modules that can be redeployed in different ways and at different times.

(5) Fortuitous, useful phenotypic gestalts (interactive wholes) arise from the collective action of dozens or hundreds of genes. The individual genes will often be conserved, duplicated, modified, and reused in future generations.

(6) Sudden, emergent innovations, as well as infinitesimal and gradual fine-tuning of those changes, represent complementary aspects of Natural Selection.

Theories about the origin of life on Earth have evolved considerably since 1953, when Miller and Urey performed an experiment that produced some rudimentary organic molecules by simulating hypothetical conditions of early planet Earth. This, combined with the discovery of DNA, RNA, and the “genetic code”, led to a family of hypotheses—known as the “Prebiotic Soup” (PBS)—that have dominated the field. However, recent empirical discoveries in geology and biochemistry led to a fundamentally new family of hypotheses that postulate that life began at “undersea alkaline hydrothermal mounds” (UAHM). These hypotheses generally provide a more cogent explanation than the PBS. The UAHM predict that the evolution of life forms resembling prokaryotic cells will be a frequent occurrence throughout the universe, but more complex life forms resembling eukaryotic cells will be relatively rare.

This chapter focuses on the implications of an updated evolutionary perspective that bridges the gap between the origin of life (Chapter 5) and its subsequent evolution. Before Natural Selection could begin to take place, the protected, energy-rich environment of undersea alkaline hydrothermal mounds (UAHM) were sufficient to serve as an incubator for the earliest forms of biological complexity to arise. Energy flux, combined with the intrinsic Emergent Evolutionary Potential (EEP) of organic compounds, drove the origins of complexity before RNA, DNA, proteins, or the “genetic code” had a chance to evolve.

Later, once macromolecules and the genetic apparatus appeared (presumably within the UAHM), Darwinian Natural Selection provided a powerful tool that accelerated evolvability, dramatically increasing the organizing power of the early life forms. Subsequent innovations provided the ability to capture energy and nutrients, maintain internal proton gradients, and ultimately escape from the UAHM and reproduce their own kinds.

That critical role for Natural Selection—providing cells (and organisms) with the organization required to capture energy and nutrients in novel ways, has continued throughout the entire history of life on Earth.

Emergent Evolutionary Potential (EEP) is a principle that applies to every imaginable level of complexity among living things. When separate species come into contact with one another, each may represent opportunities for the other to benefit in some way. This often causes the evolution of the interacting species to become intertwined. Darwin described several examples of coevolution in his On the Origin of Species, and field biologists and ecologists have found numerous remarkable examples ever since.

Even more remarkable, however, are the numerous examples in which formerly separate lineages of cells come together to form new, emergent forms of life which transcend individual species. These include composite cells, composite organisms, and composite genomes. Both EEP and classical Darwinian mechanisms play a synergistic role in the evolutionary history of these transcendent forms of biological complexity.

As is true for all scientific pioneers, Charles Darwin drew upon the theories and discoveries of those who came before him and expanded and modified those theories using his own discoveries. Darwin was not the first to propose that species change over time. Based in part on his voyage of discovery aboard the HMS Beagle, and in part on other theories such as those of Gradualism and Malthusian competition, Darwin proposed that new species arise in the struggle for existence by natural forces. His major contribution was publication of On the Origin of Species in 1859 which provided strong evidence to support his new theory of Natural Selection.

In 1866, Gregor Mendel published some early insights into the nature and transmission of hereditary factors. Mendel’s Laws of Heredity, as they are known today, resulted from his brilliant experimental design and his diligent accounts of his detailed observations.

Both Darwin’s and Mendel’s theories represent the foundations for evolutionary theory, but they were limited by the knowledge-base and empirical methodology of their times.

Mendelian Genetics truly came of age in the first decades of the 20^th century when, armed with the new Chromosomal Theory of Inheritance, Thomas Hunt Morgan and colleagues utilized powerful new experiments in fruitflies to link Mendel’s Laws to the behavior of genes carried by chromosomes, during sexual reproduction.

The “Modern Synthesis” of the 1940s combined the theory of Natural Selection with the expanded understanding of Mendelian Genetics. The statistical behavior of alleles in natural populations linked Darwin’s concept of speciation to changes in the frequencies of specific alleles.

Through the 1950s and 1960s, the abstract concepts of alleles and phenotypes were combined with subsequent discoveries concerning the molecular interactions that translate DNA sequences into specific proteins, ushering in the age of Molecular Genetics.

The discovery that DNA is the genetic material of all living things led to the discovery of its structure. Protein synthesis was shown to take place on ribosomes. Messenger RNA links DNA sequences to amino acid sequences during protein synthesis, and transfer RNA carries individual amino acids to the ribosomes. This led to the discovery of the “genetic code”, and by 1966 all 64 triplets (codons) of the “genetic code” were mapped to 20 specific amino acids, as well as three stop signals that terminate protein chains.

Since proteins carry out most of the diverse functions of cells and organisms, an understanding of the diverse roles of particular proteins in generating biological organization is essential for a modern understanding of evolution.

The one-to-one correspondence between sequences of codons and sequences of amino acids explained the various dominance relationships of Mendelian Genetics in terms of gene products and biochemistry. Various types of mutations and the phenotypes that they determine could now be understood in terms of diverse roles played by protein sequences in the inner-workings of cells.

Despite the extraordinary combined explanatory power of the “Modern Synthesis” and Molecular Genetics, neither can explain how cells—which all carry a complete set of identical DNA sequences—give rise to the diverse and complex structures and functions that arise, in each generation, during the development of multicellular individuals.

In multicellular species, useful elements that are modified and reused in novel ways are aptly described as members of “developmental toolkits”. These toolkits include flexible and reusable genetic components that regulate complex interactions between cells and macromolecules during development. The toolkit metaphor is also useful for exploring the flexibility and reuse of duplicated genes involved in prokaryotic metabolic networks.

Throughout the entire range of carbon-based life forms that have ever existed on planet Earth, a common theme is that their evolution has been driven by adaptations that help them to adopt particular ways of life (niches) that facilitate capture of energy and nutrients in novel ways. This leads to complex ecosystems of producers and consumers, including predators and prey.

In terms of evolvability and innovations that facilitate capture of energy and nutrients, multicellularity has several distinctive and useful features. Among these are the production of embryos, and the robust and flexible genetic determinants that allow emergence of higher levels of interaction between cells and the reproduction of complex structures and functions during their development.

High-speed analysis and comparison of genomic DNA sequences and other cutting-edge techniques show that multicellularity has arisen multiple times in the deep history of eukaryotic evolution, and that multicellular animals share common ancestors with the choanoflagellates.

Embryonic development is a process that is shaped by genetic determinants. Chromosomes contain those determinants, and each chromosome includes a long DNA molecule, where each position of the sequence is represented by one of four possibilities. These qualities lend themselves to a variety of metaphorical descriptions involving codes, information, computers, and digital data files.

But as pointed out by Gunther Stent, although the genome defines the unique characteristics of each species and each individual, the genome cannot be usefully considered to be a 1D representation of the organism’s multidimensional phenotype (or phenome).

A critical analysis of the pros and cons of various metaphors for development and for genomic DNA, and their evolution, leads to a better approximation of reality more suitable for the Updated Evolutionary Synthesis (UES).

Several metaphors, such as those that treat DNA as software code or embryos as computers that interpret digital information, have outlived their usefulness for evolutionary theory.

A more useful 21^st century perspective is that biological organization depends on shape-specific molecular interactions and binding events (SSM-IBE), which obey predictable physical and chemical principles.

When applied to the origins of life and the emergence of the genetic apparatus, SSM-IBE illustrates how simple molecular interactions lay the groundwork for more complex levels of structure and function to evolve.

Metaphors can be useful tools that help to illustrate the enduring core of Natural Selection in the context of the Updated Evolutionary Synthesis (UES), even when they have teleological overtones. Such metaphors include the blind watchmaker, the tinkerer, the Rube Goldberg device, the opportunist, the scrapyard, the toolkit, the black box, and trial-and-error.

These metaphors help to illustrate the power of a software technique known as the Genetic Algorithm (GA), which was inspired by Natural Selection.

The GA has also been used in simulations that demonstrate the creative power of genetic recombination, which does more than simply reshuffle genetic determinants.

The relationship between genotype and phenotype is a multifaceted question that has dominated evolutionary theory throughout the 20^th century and up to the present day. Genotype refers to the genetic determinants, whereas phenotypes refers to the actual organization, the structures and functions that are determined.

In most cases, the mapping between genes and biological structure and function cannot be understood solely by studying genes in isolation. Multiple genes and gene products must interact in complex ways to generate diverse biological structures and functions. The result is an organized whole which can be called the phenotypic gestalt.

But it is not enough to recognize the phenotypic whole. For multicellular organisms, it is also essential to realize that many genetic determinants reproduce biological organization during the process of development. This involves modular genetic elements that are modified and reused in various ways. The metaphor of a developmental toolkit is useful in this context.

To help clarify the distinction between actual phenotypes that result in particular individuals in particular ecological contexts, it is useful to introduce some new terms that distinguish toolkit elements from actual phenotypes. The former are referred to as the Generative Phenotype, and the latter are referred to as the Ecological Phenotype.

Darwin emphasized the origin of species, but the Updated Evolutionary Synthesis (UES) also emphasizes the reproduction of complex biological organization during development.

In multicellular organisms, the storage, transmission, and reproduction of biological organization depends on the inner-workings and coordinated interactions of multitudes of cells. A deep understanding of evolution requires a basic working knowledge of the molecular and cellular interactions that take place during development.

Much of the meaning and significance of the genetic determinants that accumulate by means of Natural Selection is manifested in the useful structures and functions that they generate during embryonic development.

Several types of changes in DNA sequences, including production of repetitive sequences, unequal crossing-over, gene duplication, point mutations and more, act on the genome in a synergistic manner. Together, they have extraordinary organizing power.

The UES recognizes that genomes have incorporated several general tools that facilitate, leverage, and accelerate genome evolution.

Darwin’s original concept of accumulation of infinitesimal changes must be supplemented with these widespread and now well-known mechanisms of evolutionary change. The “Modern Synthesis” focus on point mutations as the major source of new alleles fails to recognize numerous additional mechanisms of genomic sequence evolution. In many cases, several mechanisms have combined effects on the genome that are far more significant than any one mechanism alone.

Both genotypes and phenotypes can change in a variety of ways that leverage previous innovations. This can result in rapid addition of structures and functions that did not need to arise incrementally, but are often subsequently refined in an incremental fashion.

Sometimes, during DNA replication, the growing strands can mispair with the template strands. This mechanism, known as slipped-strand mispairing or replication slippage, represents a fundamental way that DNA sequences can expand into simple repetitive sequences that are subsequently diversified by other mechanisms such as point mutations.

Gene duplication represents one of the most widespread and significant types of genomic evolution. Duplicated genes played a crucial role in the evolution of diverse forms of life ranging from prokaryotesa to plants and animals. Most of the genes in animals are members of multigene families that arose by gene duplication events. Duplicated genes lay the groundwork for new innovations that have far more organizing power.

The keen sense of smell exhibited by dogs is largely a consequence of extensive gene duplication events in olfactory receptors.

The mammalian immune system provides a quintessential example of the sheer organizing power of the combined effects of gene duplication, V(D)J recombination, and somatic hypermutation to generate extraordinary diversity.

The following sections are included:

• Classical Darwinian Principles That Are Well-Supported by Thousands of Modern Examples
• Enduring Principles Established by the Modern Synthesis
• New Insights Provided by Molecular Genetics
• New Insights into the Origin of Life from Undersea Alkaline Hydrothermal Mounds
• Expansion of the Fossil Record and Molecular Phylogeny
• New Evidence Concerning the Deep History and Genomic Evolution of Prokaryotic and Eukaryotic Cells
• Emergent Evolutionary Potential
• Shape-Specific Molecular Interaction and Binding Events (SSM-IBE)
• Evolutionary Developmental Biology
• A Broader Perspective on Organisms, Levels of Organization, and Ecological Relationships
• Generative and Ecological Phenotypes, and Evolvability
• The Varieties of Genomic Variation
• Human Evolution and Evolutionary Psychology

The following sections are included:

• References
• Glossary
• About the Cover Photograph
• Index