Questions tagged [theoretical-biology]

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

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What are the methods to measure the surface density of animals in biology?

In biology there is a rule found by Damuth (https://www.nature.com/articles/290699a0): a relationship between the size of an animal species $l$ and its local abundance (surface density) $N/S$ $$N/S=...
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1answer
67 views

Where does this equation in the electrophysiology literature form come from?

In my studies I keep coming across the form of an equation that is used in many different mathematical models for voltage gated ion channels. The most general form I have found is in the 1977 paper ...
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Starting to learn biology [closed]

Well, I've not any biological background but I feel interested towards it. Can you biologists suggest me how to start? Like, from where I can start learning it, from the basic level. I'm from ...
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How are codocytes or target cells formed?

How are codocytes or target cells formed in conditions like Thalassemia? And why do they appear like a target(as in why is there a central red surrounded by pallor surrounded by red?)
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39 views

Classes of Graphs used in Biology

I am a student of Mathematics.Since I found no better place to ask my question I post it here. I was looking for some classes of graphs which are used in biology. I came across this particular class ...
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1answer
56 views

Is DNA from more parents (than two) better for the fitness of the offspring?

I'm designing a system (a computer system actually) and (a whole while ago) I spoke with a friend about it and he had this opinion: If you combine DNA of more parents (than 2) it's better for the ...
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1answer
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Formula for Oxygen Consumption for Atlantic Salmon (Mathematical) - insecurities regarding variable

The oxygen is calculated in mg per kg per something, so what does $h^{-1}$ stand for? hours maybe? The formula given below is an estimation of oxygen consumption for Atlantic salmon \begin{...
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1answer
88 views

A cure for radiation exposure?

Some of the greatest inventions of my lifetime have been from looking at nature and copying. I found out tadigrades in outer space have the ability to repair their own DNA when exposed to radiation ...
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Is there a consensus on the best Machine Learning model for Antimicrobial Resistance (AMR) prediction?

Prediction of bacterial resistance/susceptibility to antimicrobials (from genotypic data) using Machine Learning methods is a problem that has started receiving interest in recent years. The ...
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3answers
191 views

Isn't sexy son hypothesis circular?

Sexy son hypothesis. It states that females are attracted to certain traits in males, because these traits will be attractive in her sons either. But isn't this circular? Like "I'm attracted to that ...
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1answer
33 views

Approximate Cell Doubling Time?

If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the ...
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1answer
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Is there any independent non-DNA based information system in the cell

The information in protein is not neccessarily independent of the genome as the information of amino-acid sequence comes directly from the genome. The process of post-translational modification may ...
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What's a reasonable time constant for a mathematical model of a neuron?

Background I've been studying various mathematical models of neurons. So far I've covered the classic Hodgkin-Huxley model (to describe the potential difference of a single neuron) and the integrate ...
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1answer
29 views

Analysis of dynamic connectome data?

I have heard about existence of full brain connectome data of some worms or fishes. I have heard about GEVI - genetically engineered voltage indicators - that allow to see voltage data at subcellular ...
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48 views

What is the status of the “Free Energy Principle” as a theory of living organisms?

The free energy principle states that biological organisms maintain their order by minimizing a function called variational free energy (VFE). While it is the case that the minimum to VFE also ...
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39 views

How to derive the deactivation time constant in this model of Acetylcholine Receptor state kinetics?

I came across this simple analytical expression of time constant of deactivation in Elenes et al., 2006. How does one derive this expression $$\displaystyle\tau_\text{deactivation}\approx\frac{1}{D_+ ...
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Factors affecting which chromosome will come from the father

Tell me please. In course of biology, I remember that a man has XY chromosomes, and a woman has only X. Accordingly, depending on which chromosome comes from Father(man) Y or X, a girl (XX) or a boy (...
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1answer
40 views

The Hawk-Dove game: why is the average payoff half of the difference between reward and cost?

My question is about the well known Hawk-Dove model used in game theory. It concerns two strategies: the Hawk, which always fights the opponent, and the Dove, which does not fight and will either ...
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1answer
40 views

Calculating fraction of protein unfolded from spectroscopy data

This is a question from a homework pset of previous year. We are given the absorbance at 222nm of both a wild type and mutant protein at different temperatures. We are then asked to calculate various ...
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79 views

Are evolutionary algorithms calculated in polynomial time? [closed]

How complex are evolutionary algorithms? Also, what is the relationship between variational principles (Lagrangians, minima and maxima,) and evolutionary algorithms? Basically, how hard is it right ...
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1answer
40 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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1answer
496 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 ...
4
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1answer
74 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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2answers
171 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 ...
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2answers
48 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 ...
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1answer
75 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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1answer
90 views

How long does it take for a blocked dopamine receptor to be broken down by the body?

Do the blocked dopamine receptors get broken down by the body and if so how often ? In other words how long does it take for the dopamine receptors blocked by irreversible dopamine antagonists to ...
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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 ...
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3answers
263 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 ...
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1answer
157 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 ...
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0answers
47 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). ...
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1answer
97 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
84 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 ...
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3answers
226 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 ...
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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 ...
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1answer
44 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 ...
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2answers
129 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 ...
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1answer
133 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 ...
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2answers
106 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 ...
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1answer
91 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 ...
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0answers
31 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 ...
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1answer
130 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{...
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1answer
63 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?
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1answer
106 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{...
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30 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 ...
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1answer
114 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 ...
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67 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 (...
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1answer
36 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 ...
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167 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, ...
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1answer
53 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, $\...