Questions tagged [theoretical-biology]

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

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How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
Remi.b's user avatar
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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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How to interpret the breeders equation?

The univariate breeders equation is defined as, $\ R = h^2 s$ where $\ R $ is the response, $\ h^2 $ is the heritability (additive genetic variation), $\ s $ is the selection differential. The ...
rg255's user avatar
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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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Why does the slope of parent-offspring regression equals the heritability in the narrow sense?

Background ---- Notations and assumptions ---- let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $...
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What physics knowledge can be applied to biology of organisms and ecosystems?

In the wiki page of Biophysics: Biophysics spans all scales of biological organization, from the molecular scale to whole organisms and ecosystems. But after searching on the internet; the ...
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Short-term Lamarckism in asexual single cell organisms

I was reading through the Karr et al. (2012) whole-cell computational model. One of the things they did was to induce single-gene disruptions in their model. They observed several to be fatal, but: ...
Artem Kaznatcheev's user avatar
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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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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 (...
Remi.b's user avatar
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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 ...
Artem Kaznatcheev's user avatar
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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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Effects of selection on effective population size

Background The effective population size ($N_e$) is a central concept of evolutionary biology and is influenced by several parameters. For example: sex ratio bias affects $N_e$ $\left(N_e = \frac{...
Remi.b's user avatar
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Easy derivation of Kimura's approximation for the probability of fixation of a mutation

Kimura's approximation for the probability of fixation of a mutation under selection finds recurrent use in population genetics models till date. I am trying to understand the mathematical basis of ...
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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 ...
hello_there_andy's user avatar
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Book recommendations for algorithms used in evolutionary biology

Do you have recommendations for a book that presents the different algorithm used in theoretical evolutionary biology? I don't mean evolutionary or genetic algorithms (otherwise this question would ...
Remi.b's user avatar
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Macromolecule levels in daughter cells after fission

When a prokaryote undergoes binary fission, how are the non-DNA macromolecules distributed between the two daughter cells? This is motivated by comments on a previous question and a G+ discussion. I ...
Artem Kaznatcheev's user avatar
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Variance in Fst in the infinite island model

The most famous result in the study of structured populations come from Sewall Wright. He showed that in an island model, where each subpopulation is of size $N$ and the migration rate is $m$, then ...
Remi.b's user avatar
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Fisher's Fundamental Theorem of Natural Selection

Ronald Fisher discovered what he, with humility, called the Fundamental Theorem of Natural Selection. This theorem says (in its modern terminology): The rate of increase in the mean fitness of any ...
Remi.b's user avatar
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Book recommendations for evolutionary models

I was recently working on getting a statistical model of a DNA sequence. To do this I found that understanding evolution quantitatively seems to be quite important. I would really appreciate any book ...
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Why does the number of mutations per individuals follow a Poisson distribution?

I was reading this review. On page 11, left column, first paragraph, one can read: [..] there is a Poisson distribution of the equilibrium number of mutations per individual, if fitness effects are ...
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Does recombination increase the additive genetic variance for fitness?

On this article, first column, eighth line of the introduction: By bringing together favourable alleles from different chromosomes, sex and recombination increase the additive genetic variance for ...
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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 ...
Remi.b's user avatar
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Additive genetic variance with $n$ alleles

The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance: $$\sigma_D^2 + \sigma_A^...
Remi.b's user avatar
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Additive genetic variance with $n$ loci

The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance: $$\sigma_D^2 + \sigma_A^...
Remi.b's user avatar
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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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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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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 ...
Armatus's user avatar
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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 ...
woh's user avatar
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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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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 ...
Maxim V. Pavlov's user avatar
10 votes
1 answer
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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 ...
Remi.b's user avatar
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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 ...
Artem Kaznatcheev's user avatar
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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 ...
vonjd's user avatar
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9 votes
3 answers
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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 ...
Remi.b's user avatar
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9 votes
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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 ...
Remi.b's user avatar
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9 votes
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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 ...
Remi.b's user avatar
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8 votes
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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 ...
Remi.b's user avatar
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7 votes
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Alternatives to fittest-win and Moran processes as simple mathematical models of selection

When modeling selective sweeps as a micro-building block in models of macroevolution (not to be confused with misuses of this in creationist arguments), I use the fittest-win model of selection as a ...
Artem Kaznatcheev's user avatar
7 votes
1 answer
558 views

Computational/mathematical models for predicting phenotype from genotype

Karr, Sanghvi, et al. (2012) propose a whole-cell computational model for predicting phenotype from genotype in Mycoplasma genitalium. Their model simulates myriad cell processes such as DNA ...
Artem Kaznatcheev's user avatar
7 votes
2 answers
220 views

Stochastic parameters in population growth equations

I'm more of a mathematician than a biologist, so I had a question about an application of the population growth equation to real-life models, and thus would like to ask biologists for their insights. ...
Brenton's user avatar
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7 votes
1 answer
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Hamilton's derivation of direct fitness from his 1970 paper

In his 1970 paper "Selfish and Spiteful Behaviour in an Evolutionary Model", Hamilton uses Price's equation to derive his well-known rule $rb -c >0$. My question is about one of the steps in his ...
falsum's user avatar
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7 votes
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Within and Between Allelic Class Diversity

I am reading Charlesworth et al. 1997. They talk about diversity within and between allelic classes. Nucleotide diversities ($π$) at each neutral site were estimated from the mean of $2 \sum z_t (1-...
Remi.b's user avatar
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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 ...
seamos's user avatar
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Probability of Extinction under Genetic Drift

Here is the Wright-Fisher model of genetic drift: $$\frac{(2N)!}{k!(2N-k)!}p^kq^{2N-k} \Leftrightarrow \binom{2N}{k}p^kq^{2N-k}$$ where $\binom{2N}{k}$ is the binomial coefficient. This formula ...
Remi.b's user avatar
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5 votes
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439 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 ...
Remi.b's user avatar
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5 votes
1 answer
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Discrete vs Continuous Replicator Dynamics

The replicator eqn in the case of discrete non-overlapping generations and asexual reproduction is given by the discrete replicator eqn: $$x_i(t+1) = x_i (t)\frac{f_i(t)}{\bar f (t)}$$ where $x_i$ is ...
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Do the claims in this paper have any degree of validity?

The paper The waiting time problem in a model hominin population talks about a problem of waiting time, etc. Is the methodology of this numerical simulation, and the conclusion right or is it wrong? ...
user20212's user avatar
4 votes
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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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