Related papers: Absent daddy, but important father
An extension of coupled maps is given which allows for the growth of the number of elements, and is inspired by the cell differentiation problem. The growth of elements is made possible first by clustering the phases, and then by…
A key process in the life of any multicellular organism is its development from a single egg into a full grown adult. The first step in this process often consists of forming a tissue layer out of randomly placed cells on the surface of the…
In many animals parental gametes unite to form a zygote that develops into an adult with gonads that, in turn, produce gametes. Interruption of this germinal cycle by prezygotic or postzygotic reproductive barriers can result in two…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
Teams of cooperating sperm have been found across several vertebrate and invertebrate species, ranging from sperm pairs to massive aggregates containing hundreds of cells. Although the biochemical mechanisms involved in the aggregation…
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small…
The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddington's landscape, consisting of hills and valleys. The smooth top and…
Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the…
We generalize the standard Penna bit-string model of biological ageing by assuming that each deleterious mutation diminishes the survival probability in every time interval by a small percentage. This effect is added to the usual lethal but…
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…
We begin a systematic study of the enumerative combinatorics of mixed succession rules, which are succession rules such that, in the associated generating tree, the nodes are allowed to produce their sons at several different levels…
This paper develops a simplified model for sexual replication within the quasispecies formalism. We assume that the genomes of the replicating organisms are two-chromosomed and diploid, and that the fitness is determined by the number of…
The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form…
We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
As a first approximation, early embryos may be modeled as foams whose shape depends on the surface tensions of each cell. However it has been remarked that exist line tensions at polarized exterior cellular interfaces (apical). In order to…