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

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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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1answer
33 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 ...
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33 views

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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19 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 ...
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2answers
54 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 ...
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2answers
64 views

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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1answer
26 views

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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49 views

Effective population size and overlapping generations

From this book; If generations overlap, then the effective population size $N_e$ does not equal the population size $N$. I know mathematical formulations in order to find the effective population ...
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1answer
37 views

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 $n_l$ loci $n_a$ alleles

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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1answer
48 views

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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1answer
57 views

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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1answer
25 views

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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371 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 ...
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3answers
137 views

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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2answers
128 views

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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2answers
133 views

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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2answers
150 views

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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108 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 ...
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4answers
240 views

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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1answer
101 views

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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1answer
78 views

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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3answers
90 views

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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1answer
346 views

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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2answers
270 views

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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1answer
155 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 ...
7
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1answer
138 views

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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2answers
109 views

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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1answer
404 views

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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74 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 ...
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2answers
154 views

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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1answer
73 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 ...
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3answers
73 views

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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3answers
73 views

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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1answer
109 views

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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1answer
248 views

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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1answer
172 views

Are there natural selection experiments that quantitatively agree with theoretical modeling?

Has anyone ever conducted an evolution experiment and quantitatively compared it to theory? For example, has anyone ever put bacteria in a million petri dishes filled with antibiotics and calculated ...
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200 views

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 ...
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1answer
266 views

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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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 ...
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1answer
162 views

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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1answer
112 views

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 ...
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1answer
257 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 ...
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1answer
138 views

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 ...
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216 views

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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1answer
518 views

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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2answers
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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 ...