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

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25 views

What is the effective population size of a simple two deme metapopulation?

I am confused as to how to compute the effective population size $N_e$ of a theoretical structured population. Let's consider here a simple case study. Imagine a 2-deme metapopulation. Each deme is ...
1
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1answer
40 views

Biological meaning of Lotka-Volterra Jacobian matrices

In a book about community ecology, I learned about Lotka-Volterra models and dynamic food web models (I am not an ecologist in the first place). In one of the chapters, a Jacobian matrix of partial ...
0
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1answer
17 views

Statistical genetics: Allele frequencies that follow a Dirichlet distribution

From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population. We consider a set of $I$ loci and let $K_i$ be ...
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0answers
27 views

What model of epistasis best fit the reality?

In theoretical population genetics, it is very common to have to assume a model of epistatic interaction. The two most common models are the additive model and the multiplicative model. Additive ...
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0answers
23 views

Ewens-Watterson Test of Neutrality

The Ewens-Watterson test is one of the first test of neutrality (of no selection). Later came tests such as Tajima's D or Fu, Li's G and many other. Question Can you please make a description of how ...
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0answers
12 views

Measuring physical properties in soft tissue

I am working in a mathematical model of tumor growth in the framework of continuum mechanics. This kind of models allows to take in to account not just the tumor, but also the physical forces such as ...
3
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2answers
56 views

Exponential growth equation and bacteria

I'm a microbiologist, but I'm teaching some ecology in my intro-level course, so when we got to population growth, I thought I'd use the example of a microbial population. But, I hit a strange problem ...
3
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1answer
85 views

Guide to learning about Population biology / ecology / dynamics for a non-Biologist

I'm an applied mathematician who works in the field of feedback control systems but has been becoming interested in looking at population biology (e.g. Lotka-Volterra, Mathusian growth,etc.) from a ...
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1answer
86 views

Why are considered to be exceptions to the cell theory? [closed]

If I am not mistaken, the cell theory states that: All living organisms are made up of one or more cells Cells are the smallest units of life Cells arise from pre-existing cells Aseptate fungal ...
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1answer
41 views

A state model of sodium channels

I am studying by myself Human Physiology. I have encountered the following question: In the following given model of sodium channel with 3 states open closed blocked (which I assume means inactivated)...
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0answers
14 views

Effective population size of a continuously spread population

Is there any model to calculate (theoretical predictions) the effective population size of a continuously spread population? Imagine for example a population spread over an infinite 2D landscape. ...
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0answers
12 views

Effective population size of a metapopulation structured on a grid

Scenario Consider a rectangular metapopulation consisting of $x \cdot y$ demes, where $x$ is the number of deme horizontally and $y$ is the number of demes vertically. The population size per deme is ...
3
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2answers
81 views

Is “A” inhibiting “B” and vice-versa, a positive feedback loop?

If product A inhibits the expression of product B, and product B inhibits the expression of product A, is this a positive feedback loop? My thinking was to consider the scenario that A starts off ...
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0answers
36 views

Identity By Descent vs Identity By State

Background The concepts of Identity By Descent (IBD) vs Identity By State (IBS) are central in population genetics, yet I fail to fully wrap my head around the definitions. You can find examples ...
1
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1answer
35 views

Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating)

Background Quoting from Gillespie's book The level of inbreeding is measured by the inbreeding coefficient, $F_I$, which is the probability that two alleles in an individual are identity by ...
1
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1answer
52 views

Why is the probability of fixation of an allele equal to its frequency?

Introduction In a panmictic population, the probability of fixation of an allele at a neutral locus is equal to its frequency at that time. I will refer to this probability of fixation as calculated ...
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0answers
7 views

Dexamethasone radius of gyration source

I am looking for a source for the radius of gyration of dexamethasone in aqueous solution. Does anyone know where I could get it from? Even better would be an estimation of the Stokes radius, but the ...
4
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1answer
57 views

How can I obtain a computer readable model of Dr. Gerhard Michal's biological pathways map?

I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is ...
1
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1answer
21 views

Concentration gradients across membranes with different ions

I'm trying to gain an intuition for the dynamics of across neuronal membranes. The overarching idea here is they are controlled by ion concentration gradients across the membrane (which we can ...
2
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1answer
47 views

In theory how fast could nerve signals travel if the nerve fibre was perfectly insulated?

My question is purely theoretical and my main aim is to find out the maximum speed that a nerve signal can travel within a nervous system and and whether this speed represents the physical limit of ...
4
votes
1answer
48 views

A good software for agent based modelling?

Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions ...
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0answers
19 views

Need to solve a “pseudo-metabolic” network for rates

following problem: I have data on a certain complex association network (from monomers 1 ... 8 to complexes of all combinations, such as, 12 ... 13 ... 18 and so on until 12345678, so that I know ...
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1answer
78 views

Goodwin oscillator explained

Hello I have been reading papers about the Goodwin oscillator and I found that the equations are kind of tricky. Specially the part of the hill coefficient. In his paper "An entrainment model for ...
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0answers
23 views

Monod Kinetics--Growth of E.Coli in a Bioreactor

I am doing a study for a lab class. We are growing E. Coli in a bioreactor. We want to vary the volume of the initial biophase which we add after the substrate has been brought to 37 degrees C. My ...
1
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1answer
28 views

Does the Michaelis-Menten equation take in account the non-enzyme formation of products?

I only recently learned about the Michaelis-Menten equation recently, since I am not studying biology or anything related. Let's write the equation as $$\frac{d[P]}{dt} = V_{max} \cdot \frac{[S]}{K + [...
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0answers
66 views

How can a medical doctor use the information given by someone working in medical image computing(shape analysis)? [closed]

Sorry for the long headline! In short, I'm an academic researcher working in an area called "statistical shape analysis", which is intimately connected with medical image computing. It deals with how ...
1
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1answer
21 views

Is there a resource that has quantitative data about cell proteins?

I am a MSc student working in mathematical biology. In my thesis I am modelling diffusion of a protein that can bind to cell surface receptors. In order to simulate this I need some rough figures ...
4
votes
1answer
188 views

Population dynamics ODE with Allee Effects

From reading about Allee effects, it appears that there is a modification of the one-dimensional logistic equation to account for an allee effect given by: $$\frac{dN(t)}{dt} = rN\left(1-\frac{N}{K} \...
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1answer
81 views

What is the probability of genetic reincarnation? [closed]

Parents pass on 23 chromosomes to their children, with a 50/50 chance for each chromosome. Considering that people of a families lived over millennia in the same region the abundance of some ...
1
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1answer
43 views

Can heritability be deduced from a correlation coefficient?

I am trying to understand the concept of heritability and from what I can gather, the heritability of a factor (say birth weight) must be closely related to the correlation coefficient of that factor ...
1
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1answer
102 views

What are the basic skills required to pursue future studies in theoretical ecology? [closed]

I am a student and just about to choose a project for my Master's thesis in biology. I want to pursue studies in theoretical ecology in the future. Between field ecology and computational biology (as ...
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0answers
12 views

Where can one find completed and processed Hi-C datasets?

I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand ...
3
votes
1answer
24 views

Mechanisms and Assumptions of the Species-Area Realtionship

I would like to choose a model to use to describe a species area relationship based on plant species richness data that I have collected. Rather than choosing the power model a priori, I am ...
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0answers
46 views

Why is marginal reconstruction “more correct” than joint reconstruction in some cases?

When reconstructing the ancestral states on a phylogenetic tree given the states at the tips, there are a number of methods for performing the reconstruction. This question is about marginal and joint ...
5
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2answers
1k views

What are we missing about the real workings of the evolutionary process? [closed]

As a scientist (and a computer scientist at that) my view is that if we cannot simulate a process we have not understood it properly. I have been following the interesting field of Artificial Life for ...
5
votes
1answer
98 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
3
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0answers
52 views

Diffusion approximation to genetic drift

I am reading from the classical textbook Principles of Population Genetics, Hartl and Clark (pdf here). Introduction Let $f(p,x,t)$ denote the distribution of allele frequency $x$ at time $t$ ...
4
votes
1answer
56 views

Proof of the equivalence between two ways of defining ESS

Background Two common ways of defining what an Evolutionary Stable Strategy (ESS) are: First definition: Consider a population composed of populations playing two strategies, $\mathbf{p}$ and $\...
2
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1answer
49 views

I know how to solve these equations, but I'm not sure what t' represents?

I am investigating the Wilson Cowan neuron population model, and I can follow most of it, but I'm not sure what is meant by t' in the equation for proportion of neurons in the refractory period. The ...
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0answers
31 views

Values of Miu_max and Ks from parameter estimation?

Background I have this simple biomass growth model: $$ \mu = \mu_{max}\cdot \left(\frac{S}{K_S+S}\right) \cdot \left(\frac{1}{1+S/K_{iS}}\right) \cdot \left(\frac{K_{iP}}{K_{iP}+P}\right) \\ \frac{...
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0answers
48 views

Math backbone in biology/genetic

Are there any good books, that shows some advanced models in genetics particularly? The problem is i don't see any good math model in genetics interactions exept combinatorics. I'd like to know what ...
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0answers
38 views

metabolic heat generation and exercise intensity

Is there a relationship between bio heat equation (found here) and exercise intensity as described here That is I am trying to include the effect from exercises to the tempertaure variation in skin. I ...
2
votes
1answer
22 views

relationship between cytokines

This is for a mathematical research. I am building a model to identify severe dengue patients through the interaction of cytokines S1P,IL1b,TNFa,PAF and IL10. For this I would like to know if there ...
3
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0answers
37 views

Games with non-uniform interaction rates

Background: Many models in evolutionary game theory assume uniform interaction rates. For instance, consider the $2\times 2$ game: \begin{array}{l c c} & A & B \\ A & a & b \\ ...
3
votes
1answer
196 views

Do the claims in this paper have any degree of validity?

The paper The waiting time problem in a model hominin population talks about a problem of waiting time, etc. Is the methodology of this numerical simulation, and the conclusion right or is it wrong? ...
2
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0answers
26 views

Replicator equation for mixed strategies?

The the replicator equation is usually defined for pure strategies. More specifically, the replicator eqn for $n$ strategies is given by: \begin{equation} \dot x_{i} = x_{i} \left( \sum_{j=1}^{n} a_{...
3
votes
3answers
237 views

Can/Have cancer cells be/been used in stem cell culture lines?

Since Cancer cells have unlimited growth potential, can they be induced towards totipotency and pluripotency? If so, can cancer cells be used in stem cell culture because of similar properties of ...
5
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2answers
106 views

Stochastic parameters in population growth equations

I'm more of a mathematician than a biologist, so I had a question about an application of the population growth equation to real-life models, and thus would like to ask biologists for their insights. ...
1
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1answer
49 views

Can DNA base pairs go through each other? [closed]

Consider the simplified version of the motion one DNA base pair held together by a hydrogen bond: Use u and v to denote the displacements of the bases from their equilibrium position along the ...
2
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0answers
29 views

Metabolic control theory: proof of the summation theorem?

I'm looking for a rigorous proof of the summation theorem of metabolic control theory. The only sources I find are the original papers by Kacser and Burns 1973 and Heinrich and Rapoport 1974, both of ...