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6

The situation that you presented in which an entity A inhibits the production of another entity B which in turn inhibits A, is a positive feedback. In a network path or a loop the overall sign of the loop/path is the product of the signs of individual edges (interactions). In this case it is negative times negative which gives a positive sign to the loop. ...


3

Roche's Biochemical Pathways works as a big png image and just put labels on the map. But you could try to extract data using queries like http://biochemical-pathways.com/pol/fts/query?query=Glutarate It seems to be legal as it's not prohibited.


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There is no standard notation called Q (matrix). However in this case I think the matrix that they are referring to is the state transition matrix (similar to the adjacency matrix as mentioned by Justas in the comments, but with rates instead of just the connections). Basically you have three states (lets call them A, B and C) and there is a rate for ...


2

I try to answer your two questions briefly: Ion gradients are dependent on charge, but there exist independent transport mechanisms, extending diffusion. Trans-membrane transport proteins can specifically move only one sort of ions. Also symport or antiport exists, that can depend on gradients of other (e.g. non-charged molecules). In addition, the ...


2

Are kin selection and group selection the same thing? Yes and no. Yes: These days people tend to use the "direct fitness approach" (Taylor and Frank JTB 1996). It turns out that this is based on EXACTLY the same equation as is contextual analysis, which is the currently favored approach for measuring multilevel selection in natural populations ...


1

Considering your assumption: I'm just looking at the exponential part, where the simple exponential equation works. If we assume there's sufficient nutrients for bacteria to grow unchecked for a number of hours (more-or-less true in a real culture) In your original model you are using discrete states and fixed time steps. So, if 30 min is one ...


1

Real bacteria population will likely reach some carrying capacity that will prevent them to grow exponentially. As a consequence, the exponential model will be a good fit for early growth only but after a while, one will need to use some other model (typically a logistic model). Logistic model Here, I quickly present one standard model of logistic growth ...


1

If you are looking for a hard and fast answer, there is none. Life does not have a hard and fast definition, so it is impossible to identify something that everyone will recognize as both living and non-cellular. However, your question is answerable if you are interested in a summary of the state of the debate. All living organisms are made up of one ...


1

You're confused because you're failing to distinguish between 'identical' and 'identical by descent'. Some pairs of alleles would still be identical even in the absence of inbreeding. We model the inbreeding by classifying allele pairs as IDB - always homozygous - or not IDB - distributed according to Hardy Weinberg. The frequency of a pair of alleles ...


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Several proofs are given here (p. 9). My favorite comes from the genealogical argument: Consider the situation where there are $2N$ alleles: $A_1$, $A_2$, $A_3$ ... $A_{2N}$. By the genealogical argument, we may state that at $t = \infty$, all alleles at this locus will be direct descendants of one particular allele present at $t = 0$. Allelic variants at ...


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I know of an example in development biology. Here is an example where noise in retinoic acid gradients is required for the boundaries in the developing hindbrain to sharpen. A related result is that the zebrafish hindbrain has a protein to modulate noise, but does not reduce the noise to zero. Together these results show that noise in the retinoic acid ...



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