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

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3
votes
1answer
748 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 ...
8
votes
2answers
385 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 ...
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 ...
5
votes
1answer
791 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 ...
9
votes
1answer
326 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 ...
6
votes
2answers
227 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 ...
2
votes
1answer
231 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 ...
2
votes
2answers
244 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 ...
4
votes
1answer
116 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 ...
1
vote
3answers
86 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 ...
0
votes
3answers
80 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 ...
48
votes
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 ...
1
vote
1answer
133 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 ...
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 ...
8
votes
1answer
183 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?
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 ...
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
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 ...
12
votes
3answers
259 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
717 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 ...