Questions tagged [theoretical-biology]

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

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59 views

Is there a concrete metatheory that mathematically abstracts life processes (natural/artificial)? If none, how do we fix the showstoppers to have one? [closed]

In physics, Theory of everything "is a hypothetical, singular, all-encompassing, coherent theoretical framework of physics that fully explains and links together all physical aspects of the ...
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Genetic evolution without crossover

Can someone please point me to the origin of the system of coupled differential equations (1) in Section 2 of Shahshahani's book$^\star$? $$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$ ...
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Can deterministic and stochastic models be used to models different parts of the same phenomenon?

A biological phenomenon including two different causally dependent phenomenon occurs in the cell. (Phenomenon2 initiates as a result of phenomenon1). Phenomenon1 and phenomenon2 are linked with ...
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2answers
258 views

Is there such a science in which the knowledge of biological processes (e.g., evolution) would be mathematically axiomatized and inferred (deduced)? [duplicate]

There is the following Mathematical Challenge Twenty-three Mathematical Challenge Twenty-three: What are the Fundamental Laws of Biology? * This question will remain front and center for the next 100 ...
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18 views

Difference between heritability on the scale of liability versus the scale of observation

I was reading a paper on disease heritability ("Estimating Missing Heritability for Disease from Genome-wide Association Studies") and it struck me that I don't have a great understanding of ...
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2answers
478 views

Understanding expected mean number of breeding seasons

I've recently come across an equation for the expected mean number of breeding seasons after the first breeding season, as a function of the annual survival rate (S) and the probability of breeding, $$...
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3answers
292 views

What does it mean to quantitatively describe a cell?

To begin this question, I will quote Molecular Biology of the Cell (page 38): ... Biological systems are, ..., full of feedback loops, and the behavior of even the simplest of systems with feedback ...
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1answer
41 views

Interpreting replicator dynamic for simplest population model

Suppose the simplest population model where we track the size $y$ of a population: $$\frac{dy}{dt} = ry$$ for a positive constant $r$ and some $y$ such that $y(0) > 0$. For this population model ...
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83 views

Kleiber's law and Bergmann's rule

I was researching that deep-sea animals are much larger than their close relatives in the upper ocean (gigantism), and from what I've seen, this is due to two rules: Kleiber's law and Bergmann's rule. ...
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Calibrating mechanistic species distribution models for plants

I am interested in plant ecology. I would like to model the dynamics of the distribution of a group of Alpine plant species on a certain mountain. Let us assume that the dynamics can be described by a ...
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279 views

Remarkable attempts of studying biological systems axiomatically

I am reading Anti-Tech Revolution by Theodore Kaczynski, in the second chapter the author talks about how technology will cause problems in society and before he begins the discussion, he introduces ...
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Understanding the paper "Why war is a man's game"

I have read this article https://royalsocietypublishing.org/doi/10.1098/rspb.2018.0975 but I don't understand the mathematics which tries to explain why war is male-exclusive. In which branch of ...
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Is there any reliable data about the correlation between the size of a species and number of individuals that belong to it?

I'm curious to know if such a collection of data exists, so I could visualize it with a graph, and see how humans compare to other spieces of similar size.
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1answer
51 views

higher-order evolutionary adaptations

Most adaptations are what I'd call first-order. Cats evolve better eyesight; redwoods evolve to grow taller; male cardinals evolve attractive bright feathers. All of these changes were selected for ...
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133 views

References for historical momentum in asexual species definitions

For sexually reproducing organisms, the scope of a species is somewhat fixed by reproductive compatibility. However, this all collapses for organisms that exclusively reproduce asexually. Here, my ...
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Co-culture models of bacterial invasion: where to find them?

I am interested in models showing how pathogenic bacteria (namely Escherichia coli O157) can overcome commensal species (thus, causing a disease). This is a basic concept in biology but I can't find a ...
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1answer
51 views

Nonlinear (Quadratic) selection gradients formula

Under scenarios of stabilizing or disruptive selection, we can add a quadratic component to our model of phenotype and fitness like so. Specifically, I am not clear on where the 1/2 comes from nor do ...
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Conservation Law in Gene Regulatory Network modelling

I was going through the GRN modelling from Chemical and enzyme kinetics by D. Gonze & M. Kaufman (PDF). The gene has 2 sites for activator/repressor. It say the DNA $D_0$ combines with activator/...
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1answer
51 views

Mathematical/statistical models for forecasting population distributions of age, sex, weight, and height [closed]

I come from a mathematical background but I have no experience with the topic of mathematical biology. Are there well established mathematical/statistical models for forecasting the evolution of ...
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102 views

Does parental conflict lead to genes combining important functions with functions only advantageous for one of the parents?

In a sitation of a mother-father conflict of interests, the mother might use epigenetics to turn off some genes only advantageous for the father's genes and not her own. I thought a logical father's ...
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1answer
128 views

How does the Endoplasmic Reticulum scale with Cell Volume in Epithelial Cells?

I am working on a mathematical model of a biological tissue (drosophila pupal notum; an epithelial tissue) where the tissue is built up from cells all described by the same cellular-model. The tissue ...
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97 views

Examples for oscillatory behaviour in the human body

I'm looking for examples in the human body which show periodicity, more precisely, I'm looking for examples of oscillating reactions that occur in the human body which can be modelled using the ...
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1answer
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Can the fungal form of Malassezia morph into the fungal form of Candidia when feeling threatened? Resistance Mechanisms

Malassezia feeds on oils in the carbon chain 11-24 and Candida feeds on sugars. I recall learning that when these types of fungus feel they are under attack, they can morph. Does this mean they can ...
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1answer
91 views

Exact average molecular weight of a dsDNA basepair

I am trying to calculate the exact weight of a given dsDNA. On the Internet and the literature, different values for the av. molecular weight of one basepair are given : 660 g/mol (probably wrong), ...
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Is my understanding of the Bergmann's rule correct? (mass is secondary)

According to Wikipedia, Bergmann's rule applies because animals living in colder areas have greater surface-area-to-volume ratio. If I understand that correctly, the advantage of the bulkier bodies ...
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Estimate sex-specific survival from mark-recapture data using multi-site, sex-specific cormack-jolly-seber model?

I am interested in identifying sex-specific survival rates. I have a long-term dataset of individually marked birds from one breeding colony. Of these, I am able to genetically sex a subset. ...
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1answer
86 views

Is it possible to determine the initial population given the final one?

It is possible to determine the initial population of, say, bacteria given a measure at a later time? Let's say I use the logistic growth model $$\dot N (t) = rN(t)\left(1 - \frac{N(t)}{K}\right)$$ ...
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Quantitative Physiology Textbooks Recommendations?

I am currently completing a 2nd year (UK) Mamamilian Physiology Module and a Neuroscience Module. However, my degree is also 40% Maths and Statistics. So in order to learn the content better, I am ...
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2answers
72 views

How does gas equilibration occur in the alveolus, numerically?

I am attempting to model gas exchange across the alveolar membrane. My main question is there a direct exchange of O2 molecules for CO2 molecules? If so, then my model predicts (assuming alveolar ...
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2answers
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Does the magnitude of gene-expression changes decrease the more downstream a gene is from the origin of change?

If I have a decrease or increase in expression in one gene, will the decrease/increase in expression in the downstream genes always be of a magnitude lower than the previous ones, or can they be ...
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9 views

What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?

I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources ...
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1answer
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Examples of real biological applications of the Keller-Segel system

I am working on a model of aggregation behavior modeled with the Keller-Segel PDE system. I recently gave a talk on this and was asked what other examples there were of the Keller-Segel system. Since ...
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1answer
147 views

Does ATP production increase with oxygen availability?

I'm not a biologist so pardon any ignorance on my part. I'm working on a speculative evolution project and I'm looking to understand how the partial pressure of oxygen effects the maximum aerobic ...
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2answers
96 views

Why is the null hypothesis of trait evolution Brownian motion?

Many models of continuous trait evolution assume that traits evolve according to Brownian motion. What is the biological or physical basis for this choice? I realize there are models that do not ...
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1answer
67 views

Expected number of SNPs in a sample of size `k`

Consider a Wright-Fisher population of constant size N. We sample k haplotypes in this population. What is the expected number ...
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38 views

When cancer is detectable, how many sub-clones are there at that stage?

I have read somewhere that cancer is detectable when the number of cells reaches $10^7 - 10^9$, which probably varies according to the specific tumor. At this early stage, what is the expected number ...
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31 views

Any kind of online "molecular modeling playground"?

I'm wondering if anyone has ever made a tool to try out new molecular modeling/simulation algorithms, where the tool itself handles the "boring" tasks of loading PDB files, building chains ...
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1answer
35 views

Can there be traits which aren't possible objects of selection, e.g. beneath a "threshold of genetic noise"?

Is it possible that there are traits that might not be possible objects of the selection because of highly sensitive dependence on genotypes? The context of my thought came when I was having a ...
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35 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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46 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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1answer
69 views

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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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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29 views

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
42 views

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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41 views

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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1answer
116 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 ...
2
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2answers
63 views

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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2answers
162 views

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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