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

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2
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1answer
86 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 ...
0
votes
1answer
34 views

Can heritability be deduced from a correlation coefficient?

I am trying to understand the concept of heritability and from what I can gather, the heritability of a factor (say birth weight) must be closely related to the correlation coefficient of that factor ...
11
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0answers
89 views

What have the L-systems (Lindenmayer systems) been actually used for in biology?

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 ...
8
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0answers
93 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 ...
5
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0answers
54 views

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 ...
4
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0answers
64 views

Understanding F-statistics in population genetics

I am reading a classical Weir and Cockerham 1984 paper about Fst estimation. At the beginning (first page, right column), they define 3 statistics. $F$ is the correlation of genes within individuals ...
4
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0answers
359 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
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0answers
114 views

Eye color genetics

I am trying to find a model to link the phenotype eye color to its genotypes. I know that there exists a simple model from Davenport, which explains {brown,blue} eyes. Further, there is an extended ...
3
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0answers
64 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
3
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0answers
33 views

Games with non-uniform interaction rates

Background: Many models in evolutionary game theory assume uniform interaction rates. For instance, consider the $2\times 2$ game: \begin{array}{l c c} & A & B \\ A & a & b \\ ...
3
votes
0answers
70 views

How to understand relatedness in an infinite island model?

My understanding is that the relatedness coefficient in kin selection models measures positive assortment. That is, altruism is more likely to evolve if altruists tend to interact with other ...
3
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0answers
23 views

Is emergence connected to nature's transition between fractal regimes at different size scales?

A fractal algorithm like Mandelbrot is self-similar in all size scales. This is not the case in nature. A tree is fractal in the sense that each branch is similar to the tree as a whole. But that is ...
3
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0answers
65 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 ...
3
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0answers
84 views

Experimental techniques to measure protein-protein and protein-ligand structure and dynamics

We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking ...
2
votes
0answers
14 views

Metabolic control theory: proof of the summation theorem?

I'm looking for a rigorous proof of the summation theorem of metabolic control theory. The only sources I find are the original papers by Kacser and Burns 1973 and Heinrich and Rapoport 1974, both of ...
2
votes
0answers
54 views

Textbook for quantitative biochemistry with thermodynamics, as an alternative to Voet, Voet & Pratt (Fundamentals of Biochemistry)?

I'm looking for a great textbook on biochemistry that covers core topics: relevant aspects of thermodynamics, reaction kinetics, metabolism (e.g. krebs cycle, respiration, etc.). Ideally it would also ...
2
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0answers
36 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 ...
1
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0answers
7 views

Where can one find completed and processed Hi-C datasets?

I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand ...
1
vote
0answers
33 views

Diffusion approximation to genetic drift

Textbook I am reading from the classical textbook Principles of Population Genetics, Hartl and Clark (pdf here). Introduction $f(p,x,t)$ is the distribution of allele frequency $x$ at time $t$ ...
1
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0answers
29 views

Values of Miu_max and Ks from parameter estimation?

Background I have this simple biomass growth model: $$ \mu = \mu_{max}\cdot \left(\frac{S}{K_S+S}\right) \cdot \left(\frac{1}{1+S/K_{iS}}\right) \cdot \left(\frac{K_{iP}}{K_{iP}+P}\right) \\ ...
1
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0answers
46 views

Math backbone in biology/genetic

Are there any good books, that shows some advanced models in genetics particularly? The problem is i don't see any good math model in genetics interactions exept combinatorics. I'd like to know what ...
1
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0answers
21 views

Replicator equation for mixed strategies?

The the replicator equation is usually defined for pure strategies. More specifically, the replicator eqn for $n$ strategies is given by: \begin{equation} \dot x_{i} = x_{i} \left( \sum_{j=1}^{n} ...
1
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0answers
44 views

Variance in reproductive success and effective population size

Background The effective population size $Ne$ is the size of the Wright-Fisher population that experience the same amount of drift than the population under consideration. The higher the variance in ...
1
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0answers
29 views

Analytical Methods for Estimating Probability of Fixation

The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to ...
1
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0answers
41 views

What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explain how one can model the frequency of an allele that is under fluctuating selection (selection that varies through time). Not, thinking about fluctuating selection, there ...
1
vote
0answers
36 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 ...
1
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0answers
156 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
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0answers
55 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 ...
1
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0answers
73 views

Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
0
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0answers
18 views

Why is marginal reconstruction “more correct” than joint reconstruction in some cases?

When reconstructing the ancestral states on a phylogenetic tree given the states at the tips, there are a number of methods for performing the reconstruction. This question is about marginal and joint ...
0
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0answers
18 views

metabolic heat generation and exercise intensity

Is there a relationship between bio heat equation (found here) and exercise intensity as described here That is I am trying to include the effect from exercises to the tempertaure variation in skin. I ...
0
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0answers
25 views

What is the distribution of the expected number of lineages in a birth-death tree after time T?

I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death ...
0
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0answers
51 views

Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...
0
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0answers
82 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 ...