相关论文: Formalizing the gene centered view of evolution
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phenotypes, niches, ecosystems. We wish to argue that the evolution of life marks the end of a physics world view of law…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
We model the competition between recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, we…
This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These \emph{rate limits} link the…
The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change and ecological collapse. The field of…
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the…
We introduce several axioms which may or may not hold for any given subgraph of the directed graph of all organisms (past, present and future) where edges represent biological parenthood, with the simplifying background assumption that life…
Categorization is a fundamental function of minds, with wide ranging implications for the rest of the cognitive system. In humans, categories are shared and communicated between minds, thus requiring explanations at the population level. In…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place --…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
The genome is software because it a set of verbal instructions for a programmable computer, the ribosome. The theory of evolution now reads: evolution is the software developer responsible for the existence of the genome. We claim that this…
The inverse problem of general rough sets, considered by the present author in some of her earlier papers, in one of its manifestations is essentially the question of when an agent's view about crisp and non crisp objects over a set of…
Current evolutionary biology models usually assume that a phenotype undergoes gradual change. This is in stark contrast to biological intuition, which indicates that change can also be punctuated-the phenotype can jump. Such a jump could…
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition…