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TL;DR: There is a dearth of actual experimental evidence. However: there is at least one study that confirmed the process ([STUDY #7] - Myxococcus xanthus; by Fiegna and Velicer, 2003). Another study experimentally confirmed higher extinction risk as well ([STUDY #8] - Paul F. Doherty's study of dimorphic bird species an [STUDY #9] - Denson K. McLain). ...


21

There is a recent paper that introduced the first molecular-level whole-cell simulation. Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 DOI: 10.1016/j.cell.2012.05.044 The ...


14

The answer is chance or, even better, contingency. About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the ...


12

Cat claws are growing all the time, like horse hooves, or human nails. However, cats and horses usually use their claws/hooves, so they get shortened through mechanical action. An indoor cat may need their claws trimmed if it doesn't use them enough (that's why cats will want to scratch everywhere), or if has supernumerary toes that don't normally touch the ...


11

kmm's answer is correct; I just want to add some of my points on what kind of data should follow Gaussian distribution. Unless you know from observation that a process doesn't follow a Gaussian distribution (e.g., Poisson, binomial, etc.), then it probably does at least well enough for statistical purposes. I won't fault kmm for this statement ...


10

When I think about your question of natural examples of XOR, it pushes me to think about what type of natural environments (i.e., evolutionary pressures) would lead to the selection of an XOR equivalent. When we implemented a synthetic XOR by "double flipping" one transcription terminator as a type of gene expression "check valve" it was the case that I ...


9

Leonardo's already given you an excellent answer, but I thought I'd add my perspective. I'm a mathematical epidemiologist, so I'd at least like to believe these types of models are useful. For me, there are a number of things population dynamics models are especially useful for: Highlighting data requirements. Yes, models need data, as you've mentioned. ...


9

You raise two issues, both of which might be better suited for stats.SE, but I think the questions are suitably biological to warrant an answer here. Do most biological processes follow a Gaussian distribution? Unless you know from observation that a process doesn't follow a Gaussian distribution (e.g., Poisson, binomial, etc.), then it probably does at ...


8

Two previous answers listed many applications of population dynamics models. I want to add that they are also important for conservation of endangered species. For example classical stage-class model (Crouse et al 1987, free copy) indicate that the most effective way to protect sea turtles is reducing mortality of large juveniles. Moreover, you don't have ...


8

Yes, we can say the number of species is limited as you conjecture. However, quick estimation shows that the limitation has no apparent usefulness: A reasonable estimate of the largest known genome is 150 GB (150,000,000,000 or 1.5e11 nucleobases). The limit would be 4 raised to that power. That limit is so high that it is too large for most calculators ...


8

You can make the continuous approximation when the population size is large. As mentioned by arboviral, there are algorithms that allow you to perform stochastic simulations with discrete variables. However, these are computationally much more intensive than integration of ODEs. Moreover, analytical solutions for the master-equations (time evolution of ...


7

The smallest unit that can be selected is, of course, the single nucleotide. The most striking examples of this are Single Nucleotide Polymorphisms (SNPs), many of which confer selective (dis)advantages. To take a simple example, imagine a SNP that introduces a frameshift mutation, rendering a gene incapable of producing its protein. If that protein is ...


7

According to Deckmyn et al (2004), the primary effect of coppice management is that the fraction of total biomass in roots is relatively higher after coppicing, and that a substantial fraction of carbon in roots (~20% of root mass) is reallocated aboveground to support shoot growth in the spring following coppicing. Because of this large re-allocation, ...


7

Let's start with your definition. "Selection for traits that would be beneficial to a population of units at the expense of an individual unit possessing the trait" This is not a good definition of group selection. In reality, selection can act on groups regardless of the direction of selection at the individual level. This definition sounds to me (your ...


7

You either want a introductory book in evolutionary biology or a book that offers mathematical models of evolutionary processes. In my first class of evolutionary biology I had this textbook: Futuyama, Evolution I think it gives a good start to the field and offers a good overview of the difference subfields. If you think you already know enough about the ...


7

This question is really asking for examples, and the list of ways that knowledge of physics can be used in biology could be very long. However, here are a couple of examples: Systems ecology, especially with regard to energy and nutrient flow. This type of ecology can be strongly influenced by physics. For one example see the book Theoretical Ecosystem ...


7

Is the standard Lotka-Volterra (LV) model an exact fit for insulin-glucose (IG) dynamics? No. Can a similar model built on the same principles capture most of the essential features of the IG dynamics? Absolutely. How to capture most of the insulin-glucose dynamics using a slightly modified Lotka-Volterra model We can figure out how to change the LV ...


7

Cancer cells can be and are used in cell culture. HeLa cells were the first human cell line to be grown in culture and they were derived from a cervical tumor. That being said, Cancer cell lines would not necessarily be used for stem cell work. They have sustained too many mutations to study the type of questions that stem cells are used to study, though as ...


7

The process is self-reinforcing but the argument is not circular (no tautology implied). As soon as some male traits are considered more sexy than others, then there is selection for females to like those traits even more, which causes those traits to raise in frequency, which increases the selection for liking these traits. In other words, in this model, ...


6

Very little is known about the structure of fitness landscapes. H.A. Orr (2005; also Whitlock et al., 1995; Kryazhimskiy et al., 2009) explains that most experimental results do not actually attempt to measure the fitness landscape, but instead report just the average fitness versus time and average number of acquired adaptations versus time. This can't be ...


6

The Karr et al. paper attempts to capture most of the details in their model by combining features from the genome, transcriptome, proteome, and metabolome. This work heavily builds off of the coarse-grained models that you ask of especially on the work from Bernhard Palsson from which Markus Covert did his training. The answer to your question rests ...


6

There are a number of more recent papers dealing with phylogenetic methods in reconstructing language history as well, including work by Colin Renfrew and Quentin Atkinson. Here are two recent high-profile papers. Unfortunately, both are still behind paywalls, but even reading the list of papers they cite / that cite them would be a great way to answer your ...


6

That's an interesting conjecture about the total amount of genetic variation that is possible. I would modify a few things. First, since the size of genomes varies greatly among organisms (from 0.5 Mb to 15 Mb just for prokaryotes), there should be a fifth character in your set, representing the absence of a nucleotide. There are also issues of whether ...


6

The chaotic behaviour you are referring to (at least the one described in your link in the comments) is a property of the discrete version of the logistic equation, where you get chaotic dynamics at growth rates above ~3.55 (see the logistic map). The behaviour of this equation has been described in a classic paper by Robert May (1976). As you increase ...


6

Well, I think I found the very simple mistake I made… Looking again in my equations, I realize that (for some reason) $cor = 2 \cdot \frac{\sigma_A^2}{\sigma}$ And looking at this website, I see that the slope of the parent-offspring regression is $\frac{h_N^2}{2} = slope$ Here was my mistake!


6

First of all, there is a very heated debate about this in the field of social evolution at present, and you aren't likely to get a conclusive answer. One theorist may give you one answer, but another will vehemently disagree. I'll start by logically answering your questions in reverse order! Question 2: Can you please provide an intuitive explanation of why ...


6

First of all, here is a program which simulates the evolution of the G-matrix over multiple generations, it's a few years old (they seem to have stopped developing it) and I've only played with it briefly. This could solve how to model the evolution of the G-matrix. Fisher's fundamental theorem is a great place to start off with the theory of this: The ...


6

Adding onto AMR's answer, cancer cell lines are used extensively for research. They are typically fast to grow. HeLa Long grow to capacity of a 10cm dish within about 48hours, depending how you split them. Now some lines are different than others and each have their pros/cons but the main thing behind them is they make it possible to view the effects of ...


6

First, Allee effects (also positive density dependence) can be modelled in several different ways, and the equation you give is one example. The terms weak and strong Allee effects are in my experience used in a couple of different ways. Most often, strong density dependence is used to denote Allee effects where the per capita population growth rate can ...


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