The Molecular Tangled Bank: Not Seeing the Phylogenies for the Trees

Toy models for macroevolutionary patterns and trends

Many models have been used to simplify and operationalize the subtle but complex mechanisms of biological evolution. Toy models are gross simplifications that nevertheless attempt to retain major essential features of evolution, bridging the gap between empirical reality and formal theoretical understanding. In this paper, we examine thirteen models which describe evolution that also qualify as such toy models, including the tree of life, branching processes, adaptive ratchets, fitness landscapes, and the role of nonlinear avalanches in evolutionary dynamics. Such toy models are intended to capture features such as evolutionary trends, coupled evolutionary dynamics of phenotype and genotype, adaptive change, branching, and evolutionary transience. The models discussed herein are applied to specific evolutionary contexts in various ways that simplify the complexity inherent in evolving populations. While toy models are overly simplistic, they also provide sufficient dynamics for capturing the fundamental mechanism(s) of evolution. Toy models might also be used to aid in high-throughput data analysis and the understanding of cultural evolutionary trends. This paper should serve as an introductory guide to the toy modeling of evolutionary complexity.

Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis

Phylogenetic diagrams ("trees of life") based on computer-generated analyses of nucleic acid (DNA, RNA) or protein (amino acid residues) sequences are purported to reconstruct evolutionary history of the living organisms from which the macromolecules were isolated (1). "Horizontal gene transfer", an expression that refers to the ad hoc explanation of anomalous distribution of these macromolecular sequences, is an inferred past event to explain evolution that, even in principle, is not documentable. Although the diagrams ("phylogenies") help establish the details of relationships among important and widely distributed essential components of living systems (e.g., DNA of large and small replicons such as plasmids, viruses, genophores), chromatin, or protein enzymes that have conserved their function throughout the history of the evolutionary lineage (e.g., DNA that codes for polymerases or 16/18S ribosomal RNA), the HGT concept is an Alfred North Whiteheadian fallacy of misplaced concreteness (2). It is deeply flawed because of sets of unstated, unwarranted assumptions accepted as fact by practitioners: genomics and proteomic experts. They tend to be zoocentric and in particular anthropocentric computer scientists. Their relative lack of familiarity with the fossil record, hard-won life histories and transmission-genetics, taxonomy, physiology, metabolism, and ecology of the communities in which the organisms invariably reside, and many other aspects of life have led to codification of systematic errors in analysis of their, often superb, molecular data. Here we point to a prodigious but little-known symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time.