2,211 research outputs found
Fitness and entropy production in a cell population dynamics with epigenetic phenotype switching
Motivated by recent understandings in the stochastic natures of gene
expression, biochemical signaling, and spontaneous reversible epigenetic
switchings, we study a simple deterministic cell population dynamics in which
subpopulations grow with different rates and individual cells can
bi-directionally switch between a small number of different epigenetic
phenotypes. Two theories in the past, the population dynamics and
thermodynamics of master equations, separatedly defined two important concepts
in mathematical terms: the {\em fitness} in the former and the (non-adiabatic)
{\em entropy production} in the latter. Both play important roles in the
evolution of the cell population dynamics. The switching sustains the
variations among the subpopulation growth thus continuous natural selection. As
a form of Price's equation, the fitness increases with () natural selection
through variations and a positive covariance between the per capita
growth and switching, which represents a Lamarchian-like behavior. A negative
covariance balances the natural selection in a fitness steady state | "the red
queen" scenario. At the same time the growth keeps the proportions of
subpopulations away from the "intrinsic" switching equilibrium of individual
cells, thus leads to a continous entropy production. A covariance, between the
per capita growth rate and the "chemical potential" of subpopulation,
counter-acts the entropy production. Analytical results are obtained for the
limiting cases of growth dominating switching and vice versa.Comment: 16 page
Postcopulatory sexual selection
The female reproductive tract is where competition between the sperm of different males takes place, aided and abetted by the female herself. Intense postcopulatory sexual selection fosters inter-sexual conflict and drives rapid evolutionary change to generate a startling diversity of morphological, behavioural and physiological adaptations. We identify three main issues that should be resolved to advance our understanding of postcopulatory sexual selection. We need to determine the genetic basis of different male fertility traits and female traits that mediate sperm selection; identify the genes or genomic regions that control these traits; and establish the coevolutionary trajectory of sexes
The Algorithmic Origins of Life
Although it has been notoriously difficult to pin down precisely what it is
that makes life so distinctive and remarkable, there is general agreement that
its informational aspect is one key property, perhaps the key property. The
unique informational narrative of living systems suggests that life may be
characterized by context-dependent causal influences, and in particular, that
top-down (or downward) causation -- where higher-levels influence and constrain
the dynamics of lower-levels in organizational hierarchies -- may be a major
contributor to the hierarchal structure of living systems. Here we propose that
the origin of life may correspond to a physical transition associated with a
shift in causal structure, where information gains direct, and
context-dependent causal efficacy over the matter it is instantiated in. Such a
transition may be akin to more traditional physical transitions (e.g.
thermodynamic phase transitions), with the crucial distinction that determining
which phase (non-life or life) a given system is in requires dynamical
information and therefore can only be inferred by identifying causal
architecture. We discuss some potential novel research directions based on this
hypothesis, including potential measures of such a transition that may be
amenable to laboratory study, and how the proposed mechanism corresponds to the
onset of the unique mode of (algorithmic) information processing characteristic
of living systems.Comment: 13 pages, 1 tabl
The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random
Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke âdesign creationismâ to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membraneâs hydrophobic/philic nature; a selective âporeâ for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the âjackprot,â which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the âjackprot,â or highest-fitness complete-peptide sequence, required cumulative smaller âwinsâ (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (âjackdonsâ that led to âjackacidsâ that led to the âjackprotâ). The âjackprotâ is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide âeditionâ and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists
The modern versus extended evolutionary synthesis : sketch of an intra-genomic gene's eye view for the evolutionary-genetic underpinning of epigenetic and developmental evolution
Studying the phenotypic evolution of organisms in terms of populations of genes and genotypes,
the Modern Synthesis (MS) conceptualizes biological evolution in terms of 'inter-organismal'
interactions among genes sitting in the different individual organisms that constitute a population.
It 'black-boxes' the complex 'intra-organismic' molecular and developmental epigenetics mediating
between genotypes and phenotypes. To conceptually integrate epigenetics and evo-devo into
evolutionary theory, advocates of an Extended Evolutionary Synthesis (EES) argue that the MS's
reductive gene-centrism should be abandoned in favor of a more inclusive organism-centered approach.
To push the debate to a new level of understanding, we introduce the evolutionary biology
of 'intra-genomic conflict' (IGC) to the controversy. This strategy is based on a twofold rationale.
First, the field of IGC is both âgene-centeredâ and 'intra-organismic' and, as such, could build a
bridge between the gene-centered MS and the intra-organismic fields of epigenetics and evo-devo.
And second, it is increasingly revealed that IGC plays a significant causal role in epigenetic and
developmental evolution and even in speciation. Hence, to deal with the âdiscrepancyâ between
the âgene-centeredâ MS and the âintra-organismicâ fields of epigenetics and evo-devo, we sketch
a conceptual solution in terms of âintra-genomic conflict and compromiseâ â an âintra-genomic
geneâs eye viewâ that thinks in terms of intra-genomic âevolutionarily stable strategiesâ (ESSs)
among numerous and various DNA regions and elements â to evolutionary-genetically underwrite
both epigenetic and developmental evolution, as such questioning the âgene-de-centeredâ
stance put forward by EES-advocates
Biological Individuals
The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality
Universality and predictability in molecular quantitative genetics
Molecular traits, such as gene expression levels or protein binding
affinities, are increasingly accessible to quantitative measurement by modern
high-throughput techniques. Such traits measure molecular functions and, from
an evolutionary point of view, are important as targets of natural selection.
We review recent developments in evolutionary theory and experiments that are
expected to become building blocks of a quantitative genetics of molecular
traits. We focus on universal evolutionary characteristics: these are largely
independent of a trait's genetic basis, which is often at least partially
unknown. We show that universal measurements can be used to infer selection on
a quantitative trait, which determines its evolutionary mode of conservation or
adaptation. Furthermore, universality is closely linked to predictability of
trait evolution across lineages. We argue that universal trait statistics
extends over a range of cellular scales and opens new avenues of quantitative
evolutionary systems biology
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