Questions tagged [theoretical-biology]

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

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PCR: From transgene/microgram to cell concentration

I am doing research on CAR T-cell kinetics. The measurement of CAR T-cell concentrations across time is normally carried out with qPCR (see here, Fig. 1). These concentrations are generally reported ...
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What is the latest estimated probability for the self assembly of a primitive cell? [closed]

Peusner (Concepts in Bioenergetics, 1974) estimated the probability of the self-assembly of a primitive cell as $10^{-254}$. Given how much more we now know about cell biology, what is the latest ...
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Resources for understanding the basics of cell signaling, gene expression and cell fate determination, for a physics student?

I'm a physics student who will join a theoretical biology/applied mathematics research group this September. I'll link some papers at the end for further context. The main problem I have is that my ...
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7 votes
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Finding population dynamics models for multi-generational species evolution with delays

I am working on a problem from economics, to understand how populations evolve within business organizations. I have found that some of the population dynamics literature is very relevant to my own ...
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Examples of bifurcations in real-life systems

Does period-doubling bifurcation and Neimark-Sacker bifurcation happen in real-life systems? Are there some examples? I'm particularly interested in biological host-parasitoid and predator-prey models....
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What could be a refuge in host-parasitoid models

I was reading about refuge effect in host-parasitoid models and I found somewhere that refuge does not have to be only a place in habitat where hosts can hide, but also some "situation" ...
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Ecosystem Control Theory

I've used EcoNet online tool to analyze an ecosystem. You can run the default model by pressing "run model" in order to follow my question. Among the extended results there are 2 'Control ...
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27 votes
2 answers
4k views

Why don't viruses reach broad concentration outdoors in a city like allergens?

Why don't airborne viruses reach concentrations that infect most people vulnerable outdoors in a city the way an allergen can cause inflammation to everyone sensitive to it. Both are (often) ...
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How does genetic feedback shape the evolution of whole ecosystems?

While looking into the organization of ecosystems and how evolution shapes it, I've been reading "Ecology" (1975) by Eugene Odum. In chapter 6, p. 167, Odum speaks about the mutualistic ...
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Price Equation in Evolution

I am trying to solve for $\text{cov}(w_i,z_i)+E(w_i\Delta z_i)$ as it apears in Price Equations in terms of the mean $\overline{w}$ and variance $\sigma_{w}^2$ of the fitness of a population where I ...
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Difference between IC50 and Michaelis-Menten constant

I am new to biology, and getting to know the term IC50, I found that there is a connection between IC50 and Michaelis-Menten constant by the Cheng-Prusoff equation $K_{i}=\frac{\mathrm{IC}_{50}}{1+\...
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What did Masatoshi Nei 1972 mean by "However, evolution does not occur so as to assure this property at least at the nucleotide level."?

In Nei 1972 he describes what is now called Nei's standard genetic distance. This math.SE post provides an exerpt to the definition of Nei's standard genetic distance. In this paper he states In the ...
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Calculation of drug efficacy- mathematical biology approach

I am participating in a mathematical biology project. I would like to discuss the following problem: Let A be a drug such that $x_{o}$ chemical units of it kills 12% of $y$ cells per 1 day, I would ...
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2 answers
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How many cells does a single blood cell generally visit in its lifespan?

Taking the point of view of a single RBC travelling through blood vessels, approximately how many cells will it affect throughout its lifetime? As blood tends to provide O2 as a whole, I am taking &...
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Method of determining base values of traits in isolated populations

Prelude: I came across a discussion about the correct formula for calculating the average IQ of offspring, which goes something like the following $$ 100 + \frac35 \left( \left(\text{father's IQ} + \...
4 votes
2 answers
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Which approach is the common one in the literature for determining the bacterial growth rate?

I have the following data, which is OD600 (the second component) vs. time (the first component): ...
2 votes
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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 ...
2 votes
2 answers
336 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 ...
2 votes
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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 ...
6 votes
2 answers
498 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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6 votes
3 answers
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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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1 answer
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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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4 answers
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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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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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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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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 ...
3 votes
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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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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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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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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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148 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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1 answer
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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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1 answer
384 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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2 votes
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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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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 ...
5 votes
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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 ...
4 votes
2 answers
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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 ...
1 vote
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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 ...
3 votes
1 answer
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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 ...
1 vote
1 answer
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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 ...
4 votes
2 answers
151 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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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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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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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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