The modeling of biological processes using the tools of applied mathematics
0
votes
0answers
14 views
Have there been any mechanisms proposed for normalization in probabilistic population codes?
I heard a talk recently by Dora Angelaki about multi-sensory integration. Part of the talk was about bayesian inference with multiple noisy sources of information. I know that there has been a lot of ...
0
votes
1answer
58 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 ...
3
votes
0answers
38 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 ...
3
votes
1answer
59 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 ...
4
votes
1answer
106 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 ...
3
votes
1answer
52 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 ...
2
votes
0answers
40 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 ...
9
votes
1answer
136 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?
6
votes
1answer
88 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 ...
5
votes
1answer
145 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 ...
5
votes
1answer
82 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 ...
12
votes
3answers
153 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
322 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 ...
31
votes
1answer
543 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 ...
