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

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7
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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 ...
2
votes
2answers
200 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 ...
4
votes
2answers
199 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
1answer
157 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 ...
4
votes
4answers
298 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
118 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
126 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 ...
2
votes
3answers
97 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 ...
5
votes
1answer
199 views

Definitions and examples of some math-releated ecology branches

I would like to have an example of application and a brief description/definition (two or three lines) of the following fields. I would like to understand the exact differences between them. Other ...
3
votes
1answer
841 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
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 ...
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 ...
3
votes
2answers
471 views

Survivorship Curves: Type II curve mortality rate is not constant?

In graphs of survivorship curves, I'm seeing that the Type II curves are straight lines, and the supplementary text says that the mortality rate is constant (i.e. the slope of the line is constant). ...
4
votes
2answers
465 views

Could be an union/synergy between Math, Computer Science and Marine Biology?

I'm studing for my bachelor's degree in Natural Science and I have to chose the path for my future life. I have to chose the right kind of graduate studies. Since I love computer science, maths and ...
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 ...
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 ...
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 ...
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 ...
1
vote
1answer
170 views

Suggestions for an experiment? [closed]

I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have >to be fairly ...
2
votes
2answers
259 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
126 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
1answer
130 views

Population genetics and the fitness probability distribution. Why is the arithmetic mean all we need?

When recording change in allele frequency in diploid, bi-allelic, infinite and panmixic population we usually use this kind of equation: $\delta_p = \frac{p * q *( p (w11 - w12) + q * (w12 - ...
0
votes
3answers
82 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 ...
1
vote
3answers
89 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 ...
1
vote
1answer
93 views

Modeling yeast biochemical pathway using enzyme kinetics

I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation. I searched through some database yeast metabolome database ...
4
votes
0answers
94 views

Eye color genetics

I am trying to find a model to link the phenotype eye color to its genotypes. I know that there exists a simple model from Davenport, which explains {brown,blue} eyes. Further, there is an extended ...
1
vote
0answers
65 views

Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
2
votes
3answers
1k views

Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?

I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the "apparent" Km and Vmax includes enzyme inhibitions of which one might not be aware. ...
1
vote
1answer
138 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 ...
9
votes
1answer
349 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 ...
2
votes
2answers
493 views

What would it take to recognize a deer by its photo?

I am trying to recognize a deer by its antlers or any other means. Elaborating: I was hoping to use their antlers to recognize them but I have heard that most deers shed their antlers every year so ...
1
vote
0answers
23 views

Do the antlers re-grow in the same pattern every year? [duplicate]

I am a software engineer and I am trying to develop a system to identify a deer by its photograph. Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern ...
2
votes
1answer
238 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 ...
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 ...
0
votes
1answer
126 views

How to classify equilibrium points [closed]

I have the two differential equations: $$\frac{dN_1}{dt} = N_1(2 - N_1 - 2N_2)$$ $$\frac{dN_2}{dt} = N_2(3 - N_2 - 3N_1).$$ I worked out the equilibrium points to be at $N_1 = 0, \frac{4}{5}$ and ...
0
votes
2answers
247 views

Deterministic model of lambda-phage lysis/lysogeny [MATLAB] [closed]

Project 1 Base: Can someone please help me understand what I need from Project 1 Base code to do questions 1 and 2 from the first image? I'm new to MATLAB so a thorough explanation would be ...
9
votes
1answer
393 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 ...
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 ...
2
votes
1answer
48 views

Range of feasible coefficients in an unlimited growth model

If you are given an unlimited growth model in the form: $\frac {dP(t)}{dt} = k P(t)$ Obviously the population growth would never be unlimited, but let's presume for the moment that we are ...
3
votes
2answers
285 views

What software is there available for Quantitative structure–activity relationship (QSAR) pharmacological studies?

QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what ...
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 ...
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 ...
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
290 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
3answers
823 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 ...
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?
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
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 ...
3
votes
2answers
239 views

Short-term Lamarckism in asexual single cell organisms

I was reading through the Karr et al. (2012) whole-cell computational model. One of the things they did was to induce single-gene disruptions in their model. They observed several to be fatal, but: ...
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 ...