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

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4
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1answer
71 views

Mathematical models of lineage selection

I'm interested in the concept of lineage selection (Aboitiz, 1991) as an explanation for why traits would be selected for that enhance the rate at which evolution can occur, rather than directly ...
6
votes
2answers
132 views

Is there a biological neuron that spikes in response to hyperpolarizing currents?

As some background I've been building Electrophysiological models of neurons, and in the process stumbled upon a model, that in all respects is biologically plausible, but has a bizarre property I ...
10
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3answers
1k views

Book recommendation on population/evolutionary genetics?

I have recently been involved in collaborations that require me to model the population genetics of eukaryotic populations. I fear I may either be "re-inventing the wheel" or making conceptual ...
1
vote
3answers
116 views

Does the necessary Carbon Dioxide need to be in the atmosphere for mammals?

In the answers to this question, we've learnt that carbon dioxide is necessary for mammalian life, but is it necessary in the atmosphere/to breathe it in? Or does the act of respiration give a ...
4
votes
3answers
127 views

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 ...
4
votes
1answer
123 views

Chaos theory and population cycles of odd periodicity

I have just begun to read about Chaos theory and have come across the statement that "Period three implies chaos." My question: Does any odd period imply chaos or only 3? If so, how can populations ...
1
vote
1answer
131 views

Why sigmoid curves appear in quantitative analysis of many biological phenomena? [closed]

I know two examples: 1-The binding of hemoglobin to oxygen (binding of oxygen to one site of hemoglobin induces conformational changes which increase the affinity of the other sites for oxygen - the ...
2
votes
0answers
42 views

Is there a standard formula/calculation for sexual dimorphism?

Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use $$\frac{\text{Female value}}{\text{Male value}} -1$$ This would give negative values ...
7
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0answers
81 views

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 ...
8
votes
1answer
146 views

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 ...
2
votes
0answers
219 views

Mutation-Selection-Drift Equilibrium

mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift ...
4
votes
1answer
193 views

A colony of humans are sent to an alien world, at what point would the descendants evolve to be genetically incompatible with Earth humans? [closed]

I recently heard about the evolution of the London Underground mosquitoes, and how they have changed genetically enough that they almost can no longer reproduce with above ground mosquitos. Since this ...
4
votes
1answer
142 views

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 ...
2
votes
1answer
55 views

Why can blood vessel contraction be described as a second order system?

Suppose that the x-axis represents time, and the y-axis vessel diameter. Then this graph is claimed to roughly describe what happens when the blood pressure increases, then decreases. When the ...
8
votes
1answer
159 views

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 ...
5
votes
1answer
293 views

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 ...
7
votes
1answer
73 views

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 ...
0
votes
0answers
63 views

General time reversible model of evolution and Felsenstein model

I would like to get suggestions for the books related to General time reversible model of evolution and Felsenstein model etc. Specifically the mathematical treatment of these topics and concepts ...
1
vote
1answer
66 views

Modeling intracellular interactions between sender and receiver bacteria

I am involved in a modelling task of a biological process described as follows: -- "Objective: to model behavior of a sender receiver type system The process goes as follows Pre-signal [PS] is in ...
5
votes
2answers
114 views

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 ...
0
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0answers
24 views

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?
6
votes
1answer
271 views

What is the minimum population size that Hardy-Weinberg calculations can be applied to?

I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable ...
6
votes
1answer
126 views

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 = ...
17
votes
2answers
1k views

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 ...
3
votes
1answer
161 views

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 ...
7
votes
1answer
499 views

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 ...
3
votes
1answer
44 views

What are the application areas of Pattern formation studies specific to biology? [closed]

I was reading about reaction-diffusion processes, morphogenesis concept by Alan Turing and works of Murray in describing pattern formation on animals etc. But one question which came to my mind was ...
2
votes
0answers
51 views

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 ...
1
vote
0answers
27 views

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 ...
3
votes
1answer
63 views

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 ...
3
votes
1answer
112 views

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... ...
1
vote
1answer
63 views

Modelling how much cadmium a cell will be able to chelate with phytochelatins

I am involved in a synthetic biology project where I have to do modelling with ODEs. The biological process I want to model is the chelation of Cd2+ with phytochelatins, to know how much can be ...
2
votes
1answer
46 views

Definition of Linkage Desiquilibrium (LD)

According to wiki, linkage disequilibrium $D$ equals $$D = x_{11} - p_1\cdot q_1$$ where: $$ \begin{matrix} \text{Haplotype} & \text{Frequency}\\ A_1B_1 & x_{11}\\ ...
10
votes
3answers
100 views

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, ...
8
votes
2answers
1k views

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 ...
6
votes
1answer
82 views

Visualisation of phylogeography

I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the ...
6
votes
2answers
221 views

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 ...
5
votes
1answer
5k views

Calculation of the bacterial growth rate from a spectrophotomer growth curve

Typically the microbial growth in liquid cultures is monitored by turbidity. Data is obtained with a spectrophotometer to measure optical density at 600nm. The slope of the bacterial kinetic curve in ...
1
vote
0answers
128 views

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 ...
1
vote
0answers
47 views

Based on which criteria should i choose the control sample to calculate delta_delta_Ct

I want to calculate the gene expression of an experiment with the Delta delta Ct method. I have these results from two runs of a real time PCR (one for the GOI(Gene of Interest) and one for the ...
3
votes
1answer
33 views

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 ...
4
votes
1answer
179 views

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 ...
5
votes
1answer
51 views

Is there a good explanation for this swarming pattern?

A film clip would be helpful here. A few days ago I noticed a swarm of newly hatched flying bugs about 20 feet away from me with the sun behind them so the shape of swarming (such as it was) was easy ...
19
votes
1answer
526 views

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 ...
7
votes
2answers
425 views

Help with the Price equation

The Price equation describes mathematically the evolution of a population of units from one generation to the next. $\bar{w}\Delta \bar{z}$ = $Cov (w_i,z_i) $+$ E(w_i\Delta z_i)$ I would like ...
1
vote
1answer
50 views

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 ...
1
vote
1answer
87 views

Coalescent theory - independence of coalescent times

Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$. As I understand it, many ...
1
vote
1answer
146 views

Heterozygosity and overdominance

Consider $m$ loci with heterozygote advantage (overdominance) such that the fitness of the two homozygotes is $1-\frac{s}{2}$ and the fitness of the heterozygotes is $1+\frac{s}{2}$, where $s>0$. ...
2
votes
0answers
35 views

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 ...
2
votes
1answer
1k views

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 ...