Questions tagged [theoretical-biology]

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

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29 views

How does the human eye generate spikes?

Disclaimer: I have an academic background in computer vision but not biological vision. Background: Classical computer vision is concerned with images from cameras that have a fixed exposure time for ...
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40 views

What allows diverse ecology to thrive despite forces reducing species diversity?

Ecology and business are a useful model for understanding one another. One species fills a niche until it is outcompeted by another just as one business fills a niche until it is outcompeted by ...
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On stochastic Lotka-Volterra predator-prey model

I am currently working (as a mathematician) on some estimations involving an stochastic predator-prey type model in which some of the coefficients have been perturbed by a Brownian Motion yielding to ...
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Does the short cut of the current flu season affect the following ones?

While reading this question and reference 2 of the accepted answer another question came into my mind: If less people are carring those common viruses due to the COVID-19 measurements, does that mean, ...
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27 views

Can human pathogens present on plants become plant pathogens?

Since human pathogens sometimes live on the surface of plant leaves(read here and and here), and there are plant-pathogen microbes also living on leaf surfaces, is it possible for plant virulence ...
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Is there a way to determine corresponding differential equations from fitted Hill equation parameters

I am currently doing some work with GCaMP, a genetically encoded calcium indicator. According to the literature the Hill equation parameters for GCaMP6m is $K_d=167\pm3\, \text{nM}$ and $n=2.96\pm0.04$...
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Are the social-distancing measures implemented against SARS-CoV-2 also suppressing the spread of other viruses?

With social-distancing measures being implemented in many countries I would expect other viruses, like the ones that cause seasonal flus, to have also a hard time propagating in these circumstances. ...
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Is there any evidence that discards the possibility of an organism-aided evolution?

The theory of evolution of Darwin is mostly accepted nowadays, while Lamark theory has been abandoned. There are many experiments that show that experiences do not alter the genes or are passed to ...
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1answer
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Should I consider [H+] as substrate in MCT transport equation?

I'm trying to model the transport of lactate in cells (in both direction via Monocarboxylate transporters): [Lactate]intra + [H+] <----> [Lactate]extra + [H+] I found some data on kinetics of ...
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Range for which the Verhulst-Pearl model is a good approximate

The Verhulst-Pearl model describes the growth of a population using the differential equation, $$\frac{dN}{dt}=rN \left(\frac{K-N}{K} \right)$$ where N is the population (no. of organisms), r, the ...
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96 views

A question about entropy and Thermodynamics

According to the Second Law of Thermodynamics (also known as the laws of conversation of energy and mass), anything is an isolated system cannot increase in complexity. For example, a wearing suit ...
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Interpreting the reciprocal of $R_0$

$R_0$ is the average number of secondary cases arising from a single infectious individual in a fully susceptible population. In many of the compartmental models for epidemiology, the parameter $\...
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The role of duration of infectiousness in SIR models

I refer to J.H. Jones' Notes on R0. The basic SIR model - as described in Jones' Notes - considers three factors that make up the reproduction number: $\tau$ = the transmissibility (i.e., ...
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Are there peer-reviewed articles on the math (probabilities) of abiogenesis?

A recurrent claim from ID proponents is that the probability of abiogenesis having taken place is extremely low (take this as an example). This makes me wonder, are there peer-reviewed articles ...
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Is there a bacterium that became a virus?

Is it possible for a virus to be a descendant of a bacterium that was not through horizontal gene transfer? How I think this could happen: Suppose a species of bacteria lives in an environment where ...
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39 views

Why do E.coli form parallel clusters?

Discalimer: I am not a biologist. I am modelling E.Coli growth and in the Wikipedia gif one can see observe some groups where the bacteria are one next to each other, oriented at approximately the ...
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35 views

Modeling the production of mRNA

I have the following example of how an equation for the production of mRNA in a particular organism could look like: Consider the following equation for the production of mRNA for a gene Y. Gene Y ...
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How do we formulate the mutational load for “junk DNA”?

Question(s) Based on Joe Felsenstein's textbook, I was trying to formulate the mutational load for the majority of eukaryotic genomes that are junk DNA ($L_{most\_of\_genome}$). (See background ...
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1answer
38 views

What is the formula to calculate $R_0$ (basic reproduction number)?

What is the mathematical formula for $R_0$ and what does each variable represent? I have tried searching this to no avail.
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How do I compute the reproduction number given a differential equation?

Problem 2.3 in Introduction to Mathematical Epidemiology asks us to "compute the reproduction number" for a disease modeled by the following equation: $$I'=\frac{\alpha\beta I}{\alpha I+r}(1-I)-\mu I$...
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23 views

Tools for modelling and visualizing growth of cells

I am looking for a program/GUI app/package that would help me do simulations for cell growth. I have a microscopic mathematical model, and the scenario is basically the following: I start with a rod-...
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Is there a conformal transformation that maps the skull of Panthera tigris to the one of Panthera leo?

While visiting the Museum of Natural History in Rouen a few months ago, I was stunned by the similarity between the skulls of Panthera tigris and Panthera Leo: the overall shapes were very similar and ...
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1answer
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How to derive Hill equation (one specific part)

There is just one specific step in the derivation of the Hill equation for haemoglobin which I can't understand. Step from: $Y = \frac{(p\ce{O2})^n}{K_d + (p\ce{O2})^n}$ To: $Y = \frac{(p\ce{O2})^n}{(...
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Appropriate model to test if environmental variable is significant between two species?

I want to know if a given environmental variable has an effect on the range of two species/two groups of species. Specifically, I am interested in testing if one species has a "preference" for higher/...
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2answers
126 views

Lotka-Voltera predator prey model isocline?

In lotka voltera predator prey model, why do we get a straight isocline with variable prey/predator population for single value of corresponding predator/prey? I understand that we get the prey ...
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How to model species interactions on population size dynamic?

Here are two classical discrete time models of population size dynamic. The exponential growth model $$N_{t+1} = r\cdot N_t \qquad\qquad(1)$$ and the logistic growth model $$N_{t+1} = r\cdot N_t \...
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1answer
80 views

Confusion about Lotka_Volterra model for two competing species

Lotka-Volterra model for two competing species in Boyce's Elementary Differential Equations and Boundary Value problems' is given by: \begin{align*} \frac{dx_{1}(t)}{dt}&=r_{1}x_{1}-a_{11}x_{1}...
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1answer
72 views

Original Lotka–Volterra model

I am looking for the articles in which Lotka and Volterra published their original predator prey model. I couldn’t find the model presented in many textbooks in Lotka’s book Elements of Physical ...
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1answer
86 views

Why is there a mass limit on biological powered flight?

So, this is a thing I never fully understood. There are a lot of reasons for a flying creature to be limited in mass (though I'm unsure if I'm familiar with all of them), from energy consumption to ...
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Inheritance percentiles

I am aware that the average DNA contribution from each grandparent is 25%, while the possible range is 0%-50%. I found a source citing 18%-32% as the "normal" range but this was undefined. I assume ...
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1answer
60 views

Help on selecting 2 tests - unsure if they are paired or non-paired statistical test

I have data that measures the temperature of flowers and leaves on different plant species. These are the comparisons I am trying to make: Comparing the flower and leaf of the same plant at the same ...
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Length at which a branch 'branches'?

An image from this question (and originally from Karl Niklas' computer model) has prompted the following question: The branches in this tree divide with increasing frequency as we progress from the ...
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1answer
49 views

Growth rate oscillation in the a population of non-interacting bacteria

I have come across this theoretical paper claiming that if you start a batch culture from a single E. coli cell, the exponential growth rate of the population defined as $$k = \frac1N \frac{dN}{dt}$$ ...
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Understand SIR Model

I am quite unsure if I understand the concept of individual-based models(IBMS) in epidemiology. Is SIR model an example of IBMS?
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1answer
112 views

Where does this equation in the electrophysiology literature form come from?

In my studies I keep coming across the form of an equation that is used in many different mathematical models for voltage gated ion channels. The most general form I have found is in the 1977 paper ...
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Starting to learn biology [closed]

Well, I've not any biological background but I feel interested towards it. Can you biologists suggest me how to start? Like, from where I can start learning it, from the basic level. I'm from ...
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1answer
47 views

Classes of Graphs used in Biology

I am a student of Mathematics.Since I found no better place to ask my question I post it here. I was looking for some classes of graphs which are used in biology. I came across this particular class ...
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1answer
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Is DNA from more parents (than two) better for the fitness of the offspring?

I'm designing a system (a computer system actually) and (a whole while ago) I spoke with a friend about it and he had this opinion: If you combine DNA of more parents (than 2) it's better for the ...
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1answer
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Formula for Oxygen Consumption for Atlantic Salmon (Mathematical) - insecurities regarding variable

The oxygen is calculated in mg per kg per something, so what does $h^{-1}$ stand for? hours maybe? The formula given below is an estimation of oxygen consumption for Atlantic salmon \begin{...
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1answer
98 views

A cure for radiation exposure?

Some of the greatest inventions of my lifetime have been from looking at nature and copying. I found out tadigrades in outer space have the ability to repair their own DNA when exposed to radiation ...
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1k views

Isn't sexy son hypothesis circular?

Sexy son hypothesis. It states that females are attracted to certain traits in males, because these traits will be attractive in her sons either. But isn't this circular? Like "I'm attracted to that ...
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1answer
55 views

Approximate Cell Doubling Time?

If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the ...
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1answer
94 views

Is there any independent non-DNA based information system in the cell

The information in protein is not neccessarily independent of the genome as the information of amino-acid sequence comes directly from the genome. The process of post-translational modification may ...
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What's a reasonable time constant for a mathematical model of a neuron?

Background I've been studying various mathematical models of neurons. So far I've covered the classic Hodgkin-Huxley model (to describe the potential difference of a single neuron) and the integrate ...
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1answer
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Analysis of dynamic connectome data?

I have heard about existence of full brain connectome data of some worms or fishes. I have heard about GEVI - genetically engineered voltage indicators - that allow to see voltage data at subcellular ...
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What is the status of the “Free Energy Principle” as a theory of living organisms?

The free energy principle states that biological organisms maintain their order by minimizing a function called variational free energy (VFE). While it is the case that the minimum to VFE also ...
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How to derive the deactivation time constant in this model of Acetylcholine Receptor state kinetics?

I came across this simple analytical expression of time constant of deactivation in Elenes et al., 2006. How does one derive this expression $$\displaystyle\tau_\text{deactivation}\approx\frac{1}{D_+ ...
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1answer
58 views

The Hawk-Dove game: why is the average payoff half of the difference between reward and cost?

My question is about the well known Hawk-Dove model used in game theory. It concerns two strategies: the Hawk, which always fights the opponent, and the Dove, which does not fight and will either ...
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1answer
142 views

Calculating fraction of protein unfolded from spectroscopy data

This is a question from a homework pset of previous year. We are given the absorbance at 222nm of both a wild type and mutant protein at different temperatures. We are then asked to calculate various ...
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Are evolutionary algorithms calculated in polynomial time? [closed]

How complex are evolutionary algorithms? Also, what is the relationship between variational principles (Lagrangians, minima and maxima,) and evolutionary algorithms? Basically, how hard is it right ...

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