Tagged Questions

Questions relating to biological theory or theoretical developments that deals with biological processes.

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Are there any theories using thermodynamics/statistical mechanics or information theory principles to modelling in ecology?

So far, I've only known one: the MaxEnt theory. It uses the maximum information entropy developed by information theorist, which in turn inspired by the thermodynamics from physics, to predict the ...
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How does one calculate the amount of oxygen produced by trees?

I'm currently working on a project to measure the impact of tree planting. Calculating the amount of oxygen seems harder than I imagined. Of-course there's the type and size of the tree and the ...
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How to determine the relationship of competition or cooperation?

I am currently studying the interaction of Twitter memes (two or many), such as competition and cooperation. Is there any model or method in biology that can identify the types of the relationship, ...
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Discrete vs Continuous Replicator Dynamics

The replicator eqn in the case of discrete non-overlapping generations and asexual reproduction is given by the discrete replicator eqn: $$x_i(t+1) = x_i (t)\frac{f_i(t)}{\bar f (t)}$$ where $x_i$ is ...
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How quantitative is the theory of evolution right now? [closed]

We developed complex structures like eyes and brain, whose mechanisms rely on specific species of molecules and relevant chemical reactions. But we did not develop an enhanced night vision, the ...
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The replicator equation vs the Lotka-Volterra equation

Background The replicator equation with $n$ strategies is given by the differential equation: \dot x_{i} = x_{i} \left( \sum_{j=1}^{n} a_{ij}x_{j} - \phi \right) \qquad i = 1, \...
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Variance in reproductive success and effective population size

Background The effective population size $Ne$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration. The higher the variance in ...
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Do biological phenomena follow Gaussian statistics?

I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in this article, they test 9 - 12 rats in a control ...
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Biomolecule , DNA-RNA difference [duplicate]

Why is that a RNA has uracil in place of thymine? RNA could have thymine bases but it has uracil ? What is the reason for the presence of uracil there ?
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What is the distribution of the expected number of lineages in a birth-death tree after time T?

I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death ...
The most famous result in the study of structured populations come from Sewall Wright. He showed that in an island model, where each subpopulation is of size $N$ and the migration rate is $m$, then ...
I am reading Charlesworth et al. 1997. They talk about diversity within and between allelic classes. Nucleotide diversities ($π$) at each neutral site were estimated from the mean of $2 \sum z_t (... 1answer 197 views Why does the number of mutations per individuals follow a Poisson distribution? I was reading this review. On page 11, left column, first paragraph, one can read: [..] there is a Poisson distribution of the equilibrium number of mutations per individual, if fitness effects ... 4answers 159 views Is Insulin-Glucose dynamic Lotka-Volterra? From Wikipedia: The Lotka–Volterra equations, also known as the predator–prey equations, are a pair of first-order, non-linear, differential equations frequently used to describe the dynamics of ... 0answers 65 views Textbook for quantitative biochemistry with thermodynamics, as an alternative to Voet, Voet & Pratt (Fundamentals of Biochemistry)? I'm looking for a great textbook on biochemistry that covers core topics: relevant aspects of thermodynamics, reaction kinetics, metabolism (e.g. krebs cycle, respiration, etc.). Ideally it would also ... 0answers 77 views Understanding F-statistics in population genetics I am reading a classical Weir and Cockerham 1984 paper about Fst estimation. At the beginning (first page, right column), they define 3 statistics.$F$is the correlation of genes within individuals ... 3answers 115 views What fraction of sites are expected to be polymorphic? Question Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size$N$with a per site mutation rate of$\mu$where all individuals ... 1answer 117 views Forward versus backward numerical simulations in population genetics My question is closely related to this post. There are a number of existing platforms to perform numerical individual-based simulation in populations genetics. An almost exhaustive list of such ... 0answers 127 views What have the L-systems (Lindenmayer systems) been actually used for in biology? Wikipedia: An L-system or Lindenmayer system is a parallel rewriting system and a type of formal grammar. L-systems were introduced and developed in 1968 by Aristid Lindenmayer, a Hungarian ... 1answer 30 views Accuracy of best plant growth models? Given a plant$P$, predict its height$H$at time$t$since planting given some environmental variables$E_1, \dots, E_n$. How accurate are the state-of-the-art models for such thing? What data is ... 1answer 105 views System biology and evolution: Book-recommendations I have relatively good knowledge in evolutionary biology and in population genetics. I am getting more and more interested in the evolution of ... genetic developmental processes gene interactions ... 0answers 79 views How to understand relatedness in an infinite island model? My understanding is that the relatedness coefficient in kin selection models measures positive assortment. That is, altruism is more likely to evolve if altruists tend to interact with other altruists.... 1answer 133 views Michaelis-Menten equation type - how it is derived? Can somebody explain how is the following differential equation found? It is about the blood alcohol content. See this article (pages 3 and 4). They say the concentration of blood alcohol ... 1answer 62 views Altruism in viscous (asexual) populations The viscosity of a population is the tendency of offspring to remain near their place of birth. Taylor 1992 ("Altruism in viscous populations") provides a model to study how viscosity affects the ... 1answer 48 views Anopheles arabiensis lifespan and sporogony duration What is the longest observed lifespan of a mosquito, especially of the species Anopheles arabiensis? How long does it take for Plasmodium parasites to develop and move into the salivary glands of ... 1answer 61 views Modelling insecticide net efficacy loss [closed] I am currently doing some work on modelling the effects of treated nets usage on mosquito populations. Nets do not retain their maximum efficacy forever. They lose their chemical efficacy after about ... 1answer 79 views Better population models than the logistic equation [closed] For modelling the population of a single species in a region, the logistic equation is used $$\frac{dN}{dt} =kN\Big(1-\frac{N}{K}\Big)$$ where$N$is the number of organisms,$K$is the carrying ... 2answers 224 views Value of mathematical models in biology [closed] Sorry if this is too much of a soft question or if it is too broad for this site. As a person who has much more experience with math than biology, I've always been really interested in the ... 1answer 76 views Queller's 1985 version of Hamilton's rule Queller 1985 ("Kinship, reciprocity and synergism in the evolution of social behavior") provides a generalization of Hamilton's rule that allows for non-additivity. To accomplish that, Queller writes ... 2answers 312 views What are multicell spheroids? I'm from a maths background and I'm doing some research on mathematical models of cancer. I've come across alot of literature mentioning "multicell spheroids" in the context of avascular tumours. I ... 3answers 159 views Current along an axon When an action potential is induced on a neuron, the local transmembrane potential jumps from$E_{\mbox{rest}}$, the resting potential of the neuron, to$E_{\mbox{eq}}$, the equilibrium potential of ... 0answers 33 views Analytical Methods for Estimating Probability of Fixation The probability of fixation$P$of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to ... 1answer 1k views What is the difference between a mechanistic and a statistical predictive model? The simplest description of the difference between these two approaches that I have found are on this site who summarise the difference as: Mechanistic model: a hypothesized relationship between the ... 2answers 60 views Mathematical modelling of omics data [closed] I'm interested in modelling host-pathogen interactions using mathematics. I know there are good resources in Pubmed but seems I'm looking for a book or introductory reviews. My background in maths is ... 2answers 55 views How to compute the regression of individual fitness on individual phenotype Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma: \begin{array}{c |c |c|} & C & D \\ \hline \text{Cooperate (} C \... 1answer 122 views Are there any examples of how to apply evolutionary models? Apologies if this question it too open-ended; evolutionary biology is not my primary field. I have been reading a lot about the use of statistical mechanics in analyzing evolutionary dynamics. As an ... 1answer 93 views Basic Modelling in Quantitative Genetics I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a ... 0answers 59 views What is the probability of fixation for a mutant under fluctuating selection? Here is an answer which explain how one can model the frequency of an allele that is under fluctuating selection (selection that varies through time). Not, thinking about fluctuating selection, there ... 1answer 119 views Parameters for Fitzhugh-Nagumo model of Action Potential I'm a high school student who's currently in AP Biology, so my background in biology is quite limited. I'm interested in mathematically modelling action potentials. Doing a quick google search, I ... 1answer 141 views Biostatistics: Pollen dispersal directionality What Information am I looking for? Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around ... 1answer 82 views Modeling inclusive fitness Consider a population of two altruist with coefficient of relatedness$r$. The average inclusive fitness of this population will be$w_{0} + br -c$. Like in this example, assignment of inclusive ... 2answers 1k views What has caused life to choose this unfathomably tiny subset of all possible proteins? I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ... 0answers 23 views Is emergence connected to nature's transition between fractal regimes at different size scales? A fractal algorithm like Mandelbrot is self-similar in all size scales. This is not the case in nature. A tree is fractal in the sense that each branch is similar to the tree as a whole. But that is ... 2answers 66 views Hopeful Monsters in Plants? [closed] Does anyone know of any research/examples on Hopeful Monsters in Plants? I define Hopeful Monsters as organisms of a species that have macroevolutions to prompt new speciations. These ... 1answer 124 views What governs the distribution of blood vessels? Whenever someone is sick, doctor places 2 fingers on wrist & observes the heart-beat-rate by feeling pulses of a certain artery. To me it seems the distribution of blood vessels are pretty ... 1answer 51 views ratio between heat transfer coefficient and thermal conductivity [closed] Consider the Robin boundary condition for the diffusion/heat equation$\mathrm{u_t=a(t)u_{xx}+f(x,t)}$: $$\mathrm{-k(t)u_x(0,t)=h(t)u(0,t)}$$ or $$\mathrm{u_x(0,t)+\frac{h(t)}{k(t)}u(0,t)=0}$$ ... 2answers 114 views Core Biological concepts explained to a Computer Scientist? I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as: Evolution, Selection and Variation, to a ... 1answer 44 views Richard Goldschmidt's “systemic mutations”? [TLDR] I dont understand the fault people had/have with Richard Goldscmidt's concept of systemic mutations [/TLDR] As a preface, I am a undergrad biology student, so sorry if this is a "Stupid ... 1answer 222 views Expected time for a neutral allele to reach a frequency of$p_1$when starting at frequency$p_0\$
Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is $$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$ where ...