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

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46
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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 ...
19
votes
1answer
489 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 ...
12
votes
3answers
254 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 ...
9
votes
1answer
711 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
324 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
363 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
181 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
1answer
138 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
380 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
184 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
133 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
146 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
1answer
356 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
2answers
162 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 ...
6
votes
2answers
125 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
318 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
90 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
209 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
226 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
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
150 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 ...
6
votes
0answers
69 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
votes
1answer
190 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
779 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 ...
5
votes
2answers
86 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 ...
4
votes
4answers
280 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 ...
4
votes
1answer
111 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 ...
4
votes
1answer
74 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
3answers
393 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 ...
4
votes
1answer
50 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 ...
4
votes
1answer
114 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: ...
4
votes
1answer
113 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 ...
4
votes
1answer
137 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 ...
4
votes
1answer
106 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 ...
4
votes
1answer
45 views

How does the value of K determine number of local optima in NK model?

BACKGROUND The NK model of fitness landscape considers N states which can interact with K other states. For example N is the total number of genes in a haploid genome and K is the number of other ...
4
votes
2answers
188 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 ...
3
votes
3answers
106 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 ...
3
votes
1answer
31 views

Richard Goldschmidt's “systemic mutations”?

[TLDR] I dont understand the fault people had/have with Richard Goldscmidt's concept of systemic mutations [/TLDR] As a preface, I am a undergrad biology student, so sorry if this is a "Stupid ...
3
votes
1answer
109 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... ...
3
votes
1answer
29 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 ...
3
votes
1answer
723 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 ...
3
votes
1answer
60 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
154 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 ...
3
votes
1answer
226 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 ...
3
votes
0answers
79 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
2answers
185 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 ...
2
votes
1answer
64 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 ...
2
votes
1answer
100 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 ...
2
votes
2answers
236 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 ...
2
votes
1answer
68 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 ...