The logic of virus evolution
Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses
are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked …
are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked …
Viruses defined by the position of the virosphere within the replicator space
Originally, viruses were defined as miniscule infectious agents that passed through filters
that retain even the smallest cells. Subsequently, viruses were considered obligate …
that retain even the smallest cells. Subsequently, viruses were considered obligate …
On the roles of function and selection in evolving systems
Physical laws—such as the laws of motion, gravity, electromagnetism, and thermodynamics—
codify the general behavior of varied macroscopic natural systems across space and time …
codify the general behavior of varied macroscopic natural systems across space and time …
Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display
high genetic mobility. How this variability and mobility occurs remains largely unknown …
high genetic mobility. How this variability and mobility occurs remains largely unknown …
Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire
All cellular life forms are afflicted by diverse genetic parasites, including viruses and other
types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence …
types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence …
Evolutionary genomics of defense systems in archaea and bacteria
Evolution of bacteria and archaea involves an incessant arms race against an enormous
diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most …
diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most …
Toward a theory of evolution as multilevel learning
We apply the theory of learning to physically renormalizable systems in an attempt to outline
a theory of biological evolution, including the origin of life, as multilevel learning. We …
a theory of biological evolution, including the origin of life, as multilevel learning. We …
Comparative genomics of defense systems in archaea and bacteria
Our knowledge of prokaryotic defense systems has vastly expanded as the result of
comparative genomic analysis, followed by experimental validation. This expansion is both …
comparative genomic analysis, followed by experimental validation. This expansion is both …
Global organization and proposed megataxonomy of the virus world
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve
with nearly all forms of cellular life. The route of virus replication and protein expression is …
with nearly all forms of cellular life. The route of virus replication and protein expression is …
The LUCA and its complex virome
The last universal cellular ancestor (LUCA) is the most recent population of organisms from
which all cellular life on Earth descends. The reconstruction of the genome and phenotype …
which all cellular life on Earth descends. The reconstruction of the genome and phenotype …