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

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52
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2answers
2k views

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 ...
27
votes
2answers
684 views

What are the trajectories of flying insects?

Many flying insects tend to have very jagged trajectories. For moves of a fruit fly looks like a random walk. Is there any research on the properties of trajectories (e.g. their fractal dimension or ...
19
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1answer
504 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 ...
16
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 ...
12
votes
3answers
273 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 ...
11
votes
1answer
123 views

Biostatistics: Pollen dispersal directionality

What Information am I looking for? Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around ...
10
votes
3answers
881 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 ...
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, ...
10
votes
1answer
191 views

(How) does coppicing fundamentally alter tree growth?

I am interested in adding the ability to model coppice tree production to a model of perennial crops (Miguez et al 2008).. Implementing the biomass pools and allocation parameters required for tree ...
9
votes
1answer
743 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 ...
9
votes
1answer
351 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 ...
9
votes
1answer
394 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 ...
8
votes
1answer
186 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?
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 ...
8
votes
1answer
145 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 ...
8
votes
2answers
405 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 ...
8
votes
1answer
194 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 ...
8
votes
1answer
145 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 ...
7
votes
2answers
182 views

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 ...
7
votes
2answers
409 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 ...
7
votes
1answer
83 views

What is the difference between a mechanistic and a statistical predictive model?

The simplest description of the difference between these two approaches that I have found are on this site who summarise the difference as: Mechanistic model: a hypothesized relationship between the ...
7
votes
1answer
470 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 ...
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 ...
7
votes
2answers
169 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 ...
7
votes
1answer
67 views

Basic Modelling in Quantitative Genetics

I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a ...
7
votes
3answers
66 views

Current along an axon

When an action potential is induced on a neuron, the local transmembrane potential jumps from $E_{\mbox{rest}}$, the resting potential of the neuron, to $E_{\mbox{eq}}$, the equilibrium potential of ...
7
votes
0answers
76 views

Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$

Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is $$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$ where ...
7
votes
0answers
79 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 ...
6
votes
3answers
825 views

How exactly are game theoretical evolutionary models described during implementation for computer simulations?

When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of "The ...
6
votes
2answers
129 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 ...
6
votes
1answer
258 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
48 views

Parameters for Fitzhugh-Nagumo model of Action Potential

I'm a high school student who's currently in AP Biology, so my background in biology is quite limited. I'm interested in mathematically modelling action potentials. Doing a quick google search, I ...
6
votes
1answer
632 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
6
votes
1answer
332 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 ...
6
votes
2answers
102 views

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 ...
6
votes
2answers
108 views

How are Genetic Circuits Modelled?

I've read a recent Nature Methods paper by Moon T.S. et al, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure ...
6
votes
1answer
52 views

Queller's 1985 version of Hamilton's rule

Queller 1985 ("Kinship, reciprocity and synergism in the evolution of social behavior") provides a generalization of Hamilton's rule that allows for non-additivity. To accomplish that, Queller writes ...
6
votes
2answers
124 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 ...
6
votes
2answers
166 views

Hamilton's inclusive fitness approach

The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients. To build his model, Hamilton ...
6
votes
1answer
123 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 = ...
6
votes
2answers
219 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 ...
6
votes
2answers
232 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 ...
6
votes
1answer
81 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
1answer
292 views

Models of quorum sensing for multi-agent systems

Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model ...
6
votes
1answer
119 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 ...
6
votes
1answer
154 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 ...
5
votes
2answers
998 views

What has caused life to choose this unfathomably tiny subset of all possible proteins?

I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ...
5
votes
1answer
4k 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 ...
5
votes
1answer
264 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 ...
5
votes
1answer
861 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 ...