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

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4
votes
3answers
74 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 ...
1
vote
1answer
17 views

Kinetics and de novo protein prediction

De novo conformation predictors usually function by producing candidate conformations (decoys) and then choosing amongst them based on their thermodynamic stability and energy state. Most successful ...
2
votes
1answer
47 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 ...
0
votes
0answers
34 views

Adaptation by standing genetic variation and fitness variance [duplicate]

I've read a couple of paper on Fisher's Fundamental Theory of Natural selection that states: $W(t+1) = W(t) + Var_{W}(t)$ Given a population with some degree of genetic variability, and assuming that ...
6
votes
1answer
90 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 ...
17
votes
4answers
2k views

Book recommendation on population/evolutionary genetics?

I have recently been involved in collaborations that require me to model the population genetics of eukaryotic populations. I fear I may either be "re-inventing the wheel" or making conceptual ...
3
votes
0answers
27 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 ...
5
votes
2answers
200 views

Empirical evidence for Group Selection?

A controversial concept in Biology "Group Selection", has caused confusion and conflict amongst scientists since the since the mid 1990s. The more general realm of study is termed the "unit of ...
1
vote
2answers
211 views

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 ...
1
vote
1answer
42 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
votes
1answer
18 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 ...
1
vote
0answers
28 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 ...
12
votes
4answers
381 views

When are population dynamics models useful?

When are population dynamics models useful? There seems to have been a lot of research about it, but how does it help? If I need data about how a population will evolve under what conditions, I need ...
3
votes
1answer
88 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 ...
0
votes
0answers
28 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 ...
0
votes
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 ...
2
votes
2answers
313 views

Are there natural selection experiments that quantitatively agree with theoretical modeling? [closed]

Has anyone ever conducted an evolution experiment and quantitatively compared it to theory? For example, has anyone ever put bacteria in a million petri dishes filled with antibiotics and calculated ...
2
votes
1answer
144 views

Mutation-drift equilibrium and among loci variance in heterozygosity

At mutation-drift balance, the increased heterozygosity brought by new mutations is exactly equal to the loss of heterozygosity due to genetic drift. At equilibrium, the expected heterozygosity for a ...
-2
votes
1answer
108 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 ...
0
votes
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)...
3
votes
2answers
83 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 ...
0
votes
0answers
13 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 ...
0
votes
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. ...
4
votes
2answers
219 views

Randomness in living systems

The point of my question is not to talk about events that are uncontrolled by living organisms. My question is about controlled randomness, or I'd like to say adaptive random process. Process that are ...
1
vote
1answer
37 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
vote
1answer
55 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 ...
9
votes
3answers
141 views

Intuitive explanation for Kin- and Group- selection

It is known from theoretician in the field of kin selection that kin selection (inclusive fitness theory) and group selection are actually two sides of the same coin. In other words, these two ...
4
votes
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 ...
0
votes
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 ...
1
vote
1answer
22 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
votes
1answer
48 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 ...
1
vote
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 ...
1
vote
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 ...
0
votes
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 ...
4
votes
1answer
192 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} \...
1
vote
1answer
29 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 + [...
1
vote
0answers
71 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
vote
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 ...
3
votes
0answers
54 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 $t$ ...
-1
votes
1answer
103 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 ...
9
votes
1answer
2k 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 ...
5
votes
1answer
104 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 ...
5
votes
1answer
159 views

The replicator equation vs the Lotka-Volterra equation

Background The replicator equation with $n$ strategies is given by the differential equation: \begin{equation} \dot x_{i} = x_{i} \left( \sum_{j=1}^{n} a_{ij}x_{j} - \phi \right) \qquad i = 1, \...
1
vote
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 ...
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 ...
1
vote
1answer
105 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 ...
1
vote
0answers
50 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 ...