# Tagged Questions

The modeling of biological processes using the tools of applied mathematics.

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### What's the max speed that humans could run? [duplicate]

Assuming humans could use all of their muscle strength at once, with no need of cooling or energy, how fast could we theoretically run?
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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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### 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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### How many traits can a multivariate breeders equation handle?

The multivariate breeders equation (MBE) by Lande predicts the change in a trait $\Delta \bar z$ (response) as $\Delta \bar z = G \beta$ where $G$ is a genetic variance-covariance matrix and ...
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### Mutation-drift equilibrium and among loci variance in heterozygosity

At mutation-drift balance, the increased heterozygosity brought by new mutations is exactly equal to the loss of heterozygosity due to genetic drift. At equilibrium, the expected heterozygosity for a ...
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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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### Defining dominance and selection in these formulae

This paper uses two equations to explain the different conditions under which sexually antagonistic genetic variance is maintained in a population, while allowing for unequal dominance, for ...
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### Does unequal dominance mean the X-chromosome should be a coldspot for antagonistic variation?

Sexually antagonistic genetic variation, in a simple model, will persist if the benefit to one sex is (near) equal to the cost in the other, otherwise the polymorphism will be selected out of the ...
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### Integration of several environmental signals

I am looking for examples of different functions that are good fit to how signals are computed in order to respond to the environment. Let's make my question more copmrehensible with an example... ...
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### How does Natural Selection Shapes 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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### Is there a difference between endorphins that are released while physical activity and sex/masturbation?

I observerd myself and I can identify two different types of "happines". First - called by me - After Pleasure : Occurs AFTER (and last long) long activity that require from me engagement focus and ...
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### Is there a realistic “family tree” model for the human population?

I would like to do some gene inheritance simulations, and I was wondering if there is an accepted model for what mating looks like in the general human population? I am not necessarily looking for 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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### Distribution of fitness in wild populations

If I get out in the wild observe wild populations and measure the distribution of fitness $f(w)$ in a given population. What will I find out? Will I observe a Gaussian distribution, a Poisson ...
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### Effects of Genetic Drift on Linkage Disequilibrium

From what I understood of @Canadianer's answer here... Genetic drift randomly causes negative or positive linkage disequilibria, by changing allele frequencies through random sampling. Natural ...
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### Source of information on the evolution of aging/senescence

Do you know a good review (published peer-reviewed or an online course or whatever) that offers a good overview of all hypothesis explaining the various patterns linked with aging? I'd like this ...
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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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### In what ways can mechanisms of apoptosis be damaged?

How many ways can an Apoptosis mechanism be made disfunctional or irreparably damaged? If a cell has damaged Apoptosis mechanisms and it divides will its daughter cells have such damage?
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### Nervous System : Signal Translation

If a device were created to monitor the nervous signals from the heart, including stable heartbeats, rapid heartbeats, etc., and this device were capable of transmitting the "stable heartbeat" to the ...
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### How to calculate the effective population size ($N_e$) with overlapping generations?

From this Source: If generations are overlapping, then the effective population size $N_e$ does not equal the population size $N$. I know mathematical formulations in order to find the effective ...
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### Effective population size when the population sizes varies from season to season

Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in ...
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### Linkage disequilibrium with multiple alleles and loci

Linkage disequilibrium $\left(D\right)$ for two bi-allelic loci is defined as: $$D=X_{11}X_{22} - X_{12}X_{21}$$ where $X_{11},\ X_{12},\ X_{21},\ X_{22}$ are the frequencies of the haplotypes ...
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### Evolution from Mating types to different sexes

Imagine a lineage of multicellular organisms that had mating types and evolved their mating types into sexes. What are the possible mechanisms that might have brought this lineage to evolve sexes from ...
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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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### What indices can we use to describe fitness landscapes?

We usually talk of smooth or rugged fitness landscape. Are there any (standard) indices to measure the "structure" of fitness landscapes? For example, one might consider the mean epistatic ...
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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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### 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 ...
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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 ...
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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 ...
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### Why and how does complexity usually tends 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 necessary increases and that ...
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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 ...
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### Biodiversity is restricted by genome combinatorics?

Me and some friends are interested in opinions for the following: Conjecture The maximum number of species must be limited by the maximum combinatorial/permutational space that can be occupied ...
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### Natural enemies boost deep evolutionary fitness?

"Two species that reduce one another's fitness on microevolutionary (short-term) timescales can increase each other's macroevolutionary (long-term) fitness" Opinions? Intuitive Examples: ...
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### Assumptions of Hamilton's rule

Which elements of the following list are assumptions of the Hamilton's rule? Population structure (non-panmictic population) Additivity = Fitness of the heterozygote equals the mean of the ...
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### How to define “evolution”?

The standard answer to: what is evolution? is: It is a change in allele frequency over time! I believe a complete definition should encompass the following concepts: mutations copy ...
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### Index of ecological niche overlap

For this question I am interested in the Pianka's Index of ecological niche overlap. What is the Pianka's Index? How does it work? How can one calculate this index? How often is it used? In what ...
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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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### 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 ...
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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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### 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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### 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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### 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 ...
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### Why did Fair Meiosis evolve?

How and why did Fair Meiosis evolve? I can hardly think that it provided a fitness advantage to the individual carrying the mutation. Why would it? Or did it evolve through lineage selection? Or was ...
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### 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 ...
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### Could sex alone drive complexity?

Imagine that complexity is measured by a positive number $f_n$. If one has no prior knowledge about the positive number $f_n$ then from Bayesian theory one can assign $\log f_n$ an "improper" uniform ...
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### Would it be possible/plausible for a type of spider to fly by weaving web between it's legs to create bat-like wings?

I've been thinking about this lately. Would it be possible for a type of spider to gain the ability to fly freely by weaving its web between it's legs and creating wings much like those of a bat? Is ...
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### Lineage selection in plasmid evolution

I've been reading through Paulsson (2002) and I am not sure what he means by "lineage selection" in the second to last section. The paper deals with plasmid replication, and mostly concentrates on the ...
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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 ...