Questions tagged [theoretical-biology]
Questions relating to biological theory or theoretical developments that deals with biological processes.
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Is there any evidence that sexual selection may lead to extinction of species?
Darwin suggested that sexual selection, especially by female choice, may counter natural selection. Theoretical models, such as a Fisherian runaway process, suggest that evolution of preference and ...
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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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What are the trajectories of flying insects?
Many flying insects tend to have very jagged trajectories. For moves of a fruit fly looks like a random walk.
Is there any research on the properties of trajectories (e.g. their fractal dimension or ...
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Natural examples of XOR functions at the cellular level
We can often think of cells as a sort of circuit on macromolecules, and can show that they can accurately and robustly implement functions like $\text{MAJ}(x_1,...,x_n)$ (return $1$ if more than half ...
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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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Why is 'Grudger' an evolutionary stable strategy?
I am currently reading 'The Selfish Gene' by Richard Dawkins, which I am sure many here have read. The topic are evolutionary stable strategies (ESS) regarding cooperation.
I apologise for the long ...
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Do biological phenomena follow Gaussian statistics?
I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in this article, they test 9 - 12 rats in a control ...
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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 ...
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What have the L-systems (Lindenmayer systems) been actually used for in biology?
From Wikipedia:
An L-system or Lindenmayer system is a parallel rewriting system and a type of formal grammar.
L-systems were introduced and developed in 1968 by Aristid Lindenmayer, a Hungarian ...
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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 ...
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Structure of fitness landscapes in the NK model
The NK model of rugged fitness landscapes consists of $N$ sites where fitness contribution of each site depends on its state $\{0,1\}$ and is epistatically affected by $K$ other sites. When defining ...
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What does fitness really mean?
Fitness is certainly the most important concept in the theory of evolution. My question does not have to do with practical measures of fitness but with the theoretical definition of it.
I am a bit ...
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Is there a program that simulates biology on a molecular level?
Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
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Biostatistics: Pollen dispersal directionality
What Information am I looking for?
Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around ...
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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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Scoring sequence against position weight matrix
I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability
If I have a sequence say "AAPGTGASMHSGLLW" how would I score it ...
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Why are there nail growth differences between humans and other mammals?
When a cat is growing, his nails are growing with him to some extent. A grown cat has a fixed nail length that is not extending.
By contrast, human finger nails just keep on growing, so we have to ...
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How does Natural Selection shape Genetic Variation?
Background
Importance of the additive genetic variance
As stated here, the fundamental theorem of Natural Selection (NS) by Fisher says:
The rate of increase in the mean fitness of any organism ...
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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, \...
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How do you calculate the time until the steady-state of a drug?
I encountered a mathematically intriguing conundrum, in that it's related to medicine but is centered around mathematics.
Suppose drug A has a half-life in the body of 30 hours. The patient takes 40mg ...
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What is the smallest scale at which blood vessels, nerves and other structures are deterministic?
Super simple question, but I can't find the answer on the Internet (and I'm in a foreign country so the library is not English.) As the title says, what is the smallest scale at which blood vessels, ...
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(How) does coppicing fundamentally alter tree growth?
I am interested in adding the ability to model coppice tree production to a model of perennial crops (Miguez et al 2008)..
Implementing the biomass pools and allocation parameters required for tree ...
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Genetic Drift: Models, assumptions and empirical observations
There two main mathematical models to describe the process of genetic drift are Moran model and Wright-Fisher model.
My questions concern the assumptions of these models, the existence of other ...
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Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$
Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is
$$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$
where ...
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When does weak selection produce qualitatively different results from strong selection?
In evolutionary game theory, it is typical to model organisms as having a base fitness that is modified slightly by the game interaction. The ratio of the game effect versus the base fitness ...
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How exactly are game theoretical evolutionary models described during implementation for computer simulations?
When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of "The ...
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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 ...
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Fisher's Geometric Model for Dummies
Fisher's geometric model is still today one of the most important and fundamental model in evolutionary biology but it seems to me that most student in evolutionary biology don't really understand it (...
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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 ...
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Is local equilibrium a reasonable assumption for evolutionary processes?
Whenever I look at discussions of fitness landscapes (in particular, Kauffman's NK model) the questions tend to resemble:
The population is at a local equilibrium, but another equilibrium of higher ...
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Hill's function for translational regulation
Transcriptional regulation is generally modeled as a Hill's function (similar to Michaelis-Menten Kinetics):
$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{R}{K+R} -\beta _{m_X}.m_X$$
Where $m_X$ is the mRNA ...
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The Assumption of Weak Selection?
I was reading this question and I failed to fully understand the introductory part of it.
The OP (@Artem Kaznatcheev) says:
Most analytic models like to assume weak selection because it allows the ...
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Model for fluctuating selection
Is there any mathematical model to predict the behaviour and long-term consequence of counter-acting selection at different time scale?
For example, let's consider the bi-allelic gene A, with alleles ...
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Examples of Differential equations in Biology
I am a mathematician currently teaching some math classes at a university. Next semester, I'll have bachelor's degree biochemistry students. I want to know where certain math tools might be needed in ...
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Can we use differential equations for population that is discrete?
Population dynamics is often modeled using ODE. For example one common model is logistic growth model:
$$\frac{dx}{dt} = k.x.\left(1-\frac{x}{C}\right)$$
where x is population size, k is rate ...
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Start studying mathematical biology from basics
I am really passionate about theoretical and quantitative biology and I would like to build my future career around this topic.
I've just got my bachelor's degree in biology (ecology) but scince I've ...
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Examples of references for mathematical approaches in bioinformatics that are applicable to linguistics?
Do you have any classic references for mathematical approaches in bioinformatics that are applicable to linguistics (or vice versa)?
EDIT
I am mainly interested in approaches to reconstruct the ...
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How much does the distance between a transcription factor binding site and a promoter influence transcription?
Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
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Smallest unit on which selection can act
Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also ...
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How to define "Quasifixation" in continuous approximation of finite population?
Background
Many models including the famous very first models derived by Sir Ronald Fisher in his early career, assume infinite population size. In an infinite population, an allele can rise in ...
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Why and how does complexity usually tend to increase through time?
The question of complexity is classic in the very first lectures of evolutionary biology where the teacher usually tries to tell the students that complexity does not necessarily increase and that ...
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