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

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1answer
29 views

How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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0answers
27 views

What is biology according to you? [closed]

Someone asked me to explain what biology means to 'Me'. I was wondering it does to others.
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1answer
44 views

Why are semi log graphs used in drug Dose response curves?

Why are Dose response curves, as well as most biological graphs shown in semi log graphs and not normal graphs? What is the advantage of semi log graphs over regular graphs? I still haven't gotten an ...
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0answers
5 views

Classification of processes in inter-cellular/molecular dynamics

I am a computer scientist working on a general problem in multi-agent (using the word agent loosely) simulation, and I wanted to see if modeling some processes that are similar to cell signaling and ...
0
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0answers
32 views

Is it possible to estimate a phylogeny via maximum likelihood with two-state characters?

I have a dataset with two-state morphological characters. I am wondering if it is possible to calculate the maximum likelihood of a phylogenetic tree for this dataset. It seems that all of the ...
4
votes
1answer
68 views

What physiological processes give rise to a linear cell survival curve?

If we plot the number of surviving cells in a structure over time (assuming no replacement), the shape of that curve should imply something about the underlying process responsible for cell death. For ...
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0answers
15 views

What are the perfect conditions for colon cancer proliferation?

Given the modern knowledge of anatomy and biology what are the things one must do in order to maximize colorectal cancer proliferation?
2
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1answer
57 views

What are the differences in the two possible methods to calculate the Hardy-Weinberg Equation?

I am more than flabbergasted by calculations of Hardy-Weinberg equilibria. The formula's theory assumes a binomal distribution of allele frequencies in a population, and hence allows the comparison of ...
2
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2answers
37 views

Interesting examples of models [closed]

I am studying the general use of models in biology in terms of methodology, applications, usefulness etc, and I would really appreciate any recommendations of some specific examples of models from any ...
2
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0answers
27 views

Learning tensors for evolutionary or developmental biology

I'm looking for book recommendations on tensor algebra for use in biology. Tensors are being used increasingly in evolutionary biology and developmental biology, it seems. For example, here is an ...
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0answers
34 views

Use of eigenvalues of Sturm-Liuville operator

I am wondering what would be application in biology where bounds on the Eigenvalues of Sturm-Linville operator would be important?
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0answers
69 views

Epidemic threshold on a directed network

I am trying to understand the equations used in a paper (https://www.nature.com/articles/srep00469.pdf) Mainly I'm trying to understand how the epidemic thershold was calculated using the ...
4
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3answers
146 views

(Reference request) Formal abstract theory of evolution? [closed]

EDIT: please feel free to suggest books that are the closest you can come up with to what I'm looking for, even if it doesn't exactly overlap! I am very well acquainted with the theory of evolution ...
0
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0answers
22 views

Is there any specific reference available for escape probability of Bacteria?

I have come across a lot of matter dealing with exit/escape probabilities of Brownian particles. I want to know is there any specific reference available that deals with escape probability of run and ...
7
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1answer
88 views

Easy derivation of Kimura's approximation for the probability of fixation of a mutation

Kimura's approximation for the probability of fixation of a mutation under selection finds recurrent use in population genetics models till date. I am trying to understand the mathematical basis of ...
3
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0answers
41 views

What is a good approximate functional form for an equation relating plant growth to sunlight?

Question is in the title. I've got daily measurements of daily mean shortwave radiation at the surface, and annual measurements of plant growth (some measure, be it height or biomass or something). ...
4
votes
1answer
81 views

Looking for the closest example of life forms similar to some mathematical patterns

Caveat: this is my first question here, it is quite interdisciplinary, but I hope to be in the correct place to ask. I am a user of Mathematics Stack Exchange since some years ago, and this question ...
3
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0answers
73 views

Is there any example, where cooperative behaviour of predators induce fear in prey population?

I am basically from math background and doing Ph.D in mathematical biology. So I am not so efficient in biology. But my problem based on cooperative behaviour of animals during hunting which is ...
-1
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3answers
109 views

In the Selfish Gene, the chapter about ESS, how do the doves spread their genes?

In his explanation of the Evolutionary Stable Strategy, in the Selfish Gene, Richard Dawkins repeats a couple of times, that a population of hawk-type males would make the ground for a dove-type ...
3
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0answers
53 views

Measurement equation of Tree-Step pathway model

I am not specialist in biology but I want to test a parameters estimation method (based on Kalman filter) on the Tree-Step pathway model, but I cannot find a document that gives the measurement ...
0
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0answers
18 views

Cell growth and lactic acid

I'm new on this forum so I apologize if I do anything wrong. I'm currently reading a book named Bioreaction engineering principles (3rd Ed.) to understand the more mathematical aspect in cell ...
1
vote
1answer
42 views

How plausible would it be for animals to normalize the birth of monozygotic twins in their reproductive cycles? [closed]

I'm currently trying to develop the world of a sci-fi story I'm working on, and a concept I've thought of adopting with the environment and characters is a common breeding system where identical twins ...
0
votes
2answers
120 views

Activity driven model threshold

So I am trying to figure out a threshold for an activity driven model. That is described in this paper: https://www.nature.com/articles/srep00469 That is I don't see how the researchers got ...
-4
votes
1answer
123 views

Can 2 people give rise to billions? Adam and Eve 2.0 [closed]

With with the advancement of GMOs the idea of giving rise to humans from 2 people is possible making questions like this invalid? How many people are required to maintain genetic diversity? With ...
0
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0answers
29 views

Any applications of mathematical shape optimization in computational medicine?

Any applications of mathematical shape optimization in computational medicine? Or is it, as it seems, more about graph theory and systems of equations?
0
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2answers
58 views

Are resonances the reason receptors work?

From Visual phototransduction - Wikipedia: When struck by a photon, 11-cis retinal undergoes photoisomerization to all-trans retinal which changes the conformation of the opsin GPCR leading to ...
1
vote
1answer
78 views

Do axonal conduction delays have a function?

I'm reading about mathematical models of biological neural networks, which can be grouped into two categories: The model accounts for the fact that a signal takes time to travel from the excitatory ...
1
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0answers
23 views

What are some good examples of open-source articles in which the synergy of two medicines is demonstrated?

I am doing research on Stochastic Cooperative Game Theory (a subfield in mathematics), which I will henceforth call SCGT for convenience. In this theory, entities can work together to receive a bigger ...
3
votes
1answer
93 views

How to give a biological interpretation to this phase portrait?

Consider the following system and analyze its behavior. $$\begin{array}{rl} \frac{dA}{dt} &= A \left( 2-\frac{A}{5000}-\frac{L}{100} \right)\\ \frac{dL}{dt} &= L \left(-\frac{1}{2}+\frac{...
-1
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1answer
51 views

Are there laws in ecology? [closed]

Are there clearly defined ecological laws, as in the science of physics? If not, why is this the case?
1
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1answer
91 views

Mathematical model about the relationship between two animal species

I'd like to relate a mathematical model with two animal species. This is the model: $$ \begin{split} \frac{dN}{dt} & =rN-\frac{rN(N+M)}{k} \\ \frac{dM}{dt} & =r'M-\frac{r'M(N+M)}{k'} \end{...
1
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0answers
27 views

What is known and what can be measured of biofilms?

Context for the question I am a mathematics researcher working on the mathematics of imaging and parameter estimation (inverse problems). I found an interesting diffusion equation that models the ...
2
votes
1answer
68 views

Evolution of leukemia pluripotent short-term cells

I have a problem in understanding the introduction of this paper entitled "Stability and bifurcation in a model for the dynamics of stem-like cells in leukemia under treatment". As I have no ...
5
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0answers
51 views

Kinetic mathematical model of glycolysis?

I am looking for papers containing kinetic mathematical models of glycolysis, hopefully in mammalian cells (or as close as possible, say yeast). The papers I have found do qualitative analysis (...
1
vote
1answer
30 views

Are pheromones capable of activating changes to the Phenotype of a complex organism?

I know that pheromones are means of communication between the same species, but are they capable of changing the phenotype of an organism, may be influencing the expression of the genes of a said ...
1
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0answers
113 views

Does the Histogen Theory apply to plant roots as well as stems?

My school textbook briefly mentions a certain "Histogen Theory" (von Hanstein) of plant growth/development. However, I can't find any authoritative source on this matter online. According to my book, ...
1
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1answer
49 views

Mathematical model for malaria

The simplest malaria model is as follows: $$\frac{dI}{dt} = \frac{\alpha \beta I}{\alpha I + r} (1-I) - \mu I$$ where $r$ is the natural death rate of mosquitoes, $\mu$ is the death rate of humans, $\...
1
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0answers
29 views

Units of parameters in epidemiological model

The simplest malaria model is given by $$\frac{dI}{dt} = \frac{\alpha \beta I}{\alpha I + r} (1-I) - \mu I$$ where $\mu$ is the death rate of humans, $\alpha$ is the transmission rate from humans to ...
0
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1answer
28 views

Are genes known or at least conjectured to evolve cyclically ?

I observed recently that some people born the same year in not too distant areas (say, in the same country whose size is not too big, like France) share similar phenotypical features, for example they ...
1
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0answers
145 views

How to correlate survival probability to gene expression profile?

I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
0
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1answer
26 views

Query regarding calculation of survival analysis

According to this tutorial, for table to find the survival estimates, the square root of the 6th column is multiplied with the 4th column, which is Survival probability. The value that should come for ...
1
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2answers
110 views

Mathematical representation of “gene signatures”

According to Wikipedia's definition, "a gene signature is a group of genes in a cell whose combined expression pattern is uniquely characteristic of a biological phenotype or medical condition." ...
5
votes
1answer
195 views

Biological meaning of taking zero as coefficient of the Laplacian in mathematical models of cell motility

Several mathematical models from theretical biology deal with various forms of cell motility (for example, cancer growth) or evolution of populations. The equations that make up such models usually ...
1
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0answers
64 views

Why Differential equation is not a good way to model chemical reaction networks [closed]

I'm a computer scientist and mostly code and have worked with Boolean models of cell level molecule transfer. Now i'm reading about the Biological pathways and modelling chemical reaction networks / ...
1
vote
1answer
80 views

Mathematical Biology Jobs/Prospects? [closed]

I'm a junior math major starting to take his first courses in Algebra, Analysis, Topology, Nonlinear and Partial Differential Equations, etc. I am just considering my career options at this point ...
3
votes
1answer
57 views

The title et al [closed]

I have found the extension "et al" with biologists from different nationalities like : Avery et al ; Taylor et al etc. My question : 1. What does it mean? 2. Why only biologists?
5
votes
1answer
83 views

Replicator dynamics giving probabilities greater than 1?

I have a linear replicator equation and I want to simulate its dynamics to find the resting point and hopefully the Nash equilibrium. I defined strategies' payoff as $ \vec f = C*\vec p+ \vec b$, ...
1
vote
1answer
46 views

Hopfield-like neuron assemblies

There seems to be general agreement that theoretical Hopfield networks (consisting of artifical neurons, namely McCulloch-Pitts neurons) are biologically rather implausible, among other reasons ...
0
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2answers
71 views

How do you derive steady-state conditions from the open-state differential equation of ion channels?

My books describes this differential equation for the open state of an ion channel: Where $k$ are the rate constants, $k_1$ denotes a forward reaction $k_{-1}$ denotes a reverse reaction in the ...
2
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2answers
67 views

Is it possible to have life that feeds on thermal energy

On earth, as far a we know, there are two main ways that bacteria gain energy. First, there is Photosynthesis, the transition of light into chemical based energies such as ATP. Second, there are ...