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11

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 ...


6

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 ...


5

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 ...


5

The frequency fluctuations will be determined by a standard model of selection as found in any basic population genetics text. In this scenario they take a very basic form: during each long period $i$ the frequency of $A_1$ increases from $f_i$ to $f_i\cdot (1+s_1)^{n_1}$ and during each short period $j$ the frequency of $A_1$ decreases from $f_j$ to ...


4

That's an interesting model, because mosquitoes are vectors for serious illnesses, so are pretty well studied. One team of scientists are working on genetically altering mosquitoes in Africa to make them unable to transmit the parasite that causes malaria. As the mosquitoes breed, it spreads through the population. In an interview, the lead researcher ...


3

The writings by Samir Okasha (philosopher of biology/science) could be a good starting point. In his book Evolution and the Levels of Selection, he explicitly uses the Price equation to discuss selection at multiple levels (e.g. chapter 2.3: Price's equation in a hierarchical setting), and also derives a multi-level version of the Price equation: ...


3

Fishers Geometric Model (FGM) is a theoretical prediction about the adaptation process in traits. There are a number of things to establish before attempting comprehend FGM. Firstly, shifts in an adaptive landscape, in natural scenarios, are generally quite small. Because populations have been evolving for such a long time and the small shifts in adaptive ...


3

I am presenting a speculative approach since nobody has mentioned about any existent models yet. Assuming that selection is based on performance in certain tasks; performance is a function of traits which in-turn is a function of genotype. Performance is a non-linear function of genotype and selection imposes a cutoff/bandpass filter on the performance ...


2

I'd like to add a few books to to the above suggestions. The book by Sean Rice "Evolutionary Theory: Mathematical and Conceptual Foundations" covers a lot of ground, including allele-based models, quantitative genetics, Price's formalism, and MLS. If you're interested in social evolutionary models, I found R. McElreath and R. Boyd "Mathematical Models for ...


2

Well, there are some questions regarding what population. I don't have 50 rep, so I can't really ask for clarifications; populations range a lot, from your typical avoidance of inbreeding (laws against cousin marriage) to Tamils with their high rates of first cousin marriage (so high that they don't have any pedigree inbreeding depression due to selection, ...


2

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 ...


2

No it isn't necessary to breathe in CO2 from the atmosphere. For the buffer system your brain detects the amount of CO2 (H+ which is an indicator of excess or too little CO2) and adjusts your breathing automatically to compensate so that your blood's pH stays normal. No outside CO2 is needed. Your kidneys also play a similar role but the lungs are what ...


2

Your logic looks correct to me. Essentially, what you are doing is uniformly distributing the regulator among the available mRNA. Note that even when using Hill functions to model transcription, the ratio of transcription factor (TF) concentration to the number of TF binding sites must be large - otherwise, you would have to consider binding ratios even at ...


2

What you are looking for sounds like the mechanism for a fold-change detector. I would recommend looking at these two papers: The incoherent feedforward loop can provide fold-change detection in gene regulation As an example of this working in a real system, I recommend looking at the NFkB pathway, as recently detailed by Suzanne Gaudet: Fold Change of ...


2

One example of what you may consider to be a macroevolutionary change is a whole-genome-duplication, or polyploidy event. These are not uncommon in plants, and can promote speciation due to a reproductive barrier arising between the polyploid progeny and the diploid parents. You can find many papers about this topic, here is one from 2009: ...


2

His notion of systemic mutations involved the postulation of massive chromosomal rearrangements (not mere recombination/crossing-over) as mediators of speciation in one-step. While whole genome duplications have been shown to induce speciation (see, for example, cryptic speciation in Hyla versicolor) they are not large scale rearrangements as he suggested. ...


2

I'm not sure I understand the question. You've elegantly demonstrated that only a tiny fraction of all protein sequences could possibly exist, but then asked why only a tiny fraction of all protein sequences do exist. Your conclusions about independent origins of life having no proteins in common are accurate, but also consider that you as a human being have ...


1

I am not sure what your question is but here is an example that may interest you. The three sunflower species Helianthus anomalus, H. deserticola, and H. paradoxus are all of hybrid origin of the same two "parent species" (H. annuus and H. petiolaris). Major ecological transitions in wild sunflowers facilitated by hybridization is a paper that will ...


1

No, mammals need not take in CO2 from atmosphere. The body's homeostatic function will maintain its composition by checking the amount of CO2 released out by lungs. So certainly animals would survive if put in a CO2 free atmosphere.


1

Fry (2010) borrowed his variables from Kidwell et al. (1977). Kidwell defines the fitness of each genotype as, $w_{m1}$, $w_{f1}$ = male and female fitness of the A$_1$A$_1$ genotype. $w_{m2}$, $w_{f2}$ = male and female fitness of the A$_1$A$_2$ genotype. $w_{m3}$, $w_{f3}$ = male and female fitness of the A$_2$A$_2$ genotype. Kidwell then establishes ...


1

Regarding the equivalence of MLS and kin selection, here is how I see the equivalence between these two approaches to selection. MLS says that cooperation is favored when the response to between-group selection outweighs within-group selection. Price's equation tells us that this happens when the genetic variance between-groups is higher than the genetic ...


1

Long for a comment but consider this to be an extended comment and not an exact answer: At least for Poisson I can say that the random variable should fit the three Poisson postulates. Poisson RV generally describe discrete events in continuous intervals. A fitness function doesn't seem to be such a type of RV; it is a property of a population rather than ...


1

There are many different ways to do this, depending on what assumptions you make on e.g. stable age structure, distribution of offspring, haploidy/diploidy, population growth etc. As you probably know, there are also two main approaches to effective population sizes, namely ones based on: the rate of inbreeding ($N_{e,i}$) the increase in variance of ...


1

Being a typical molecular biologist, I am a little uncomfortable with classical genetics terms. I might redefine some symbols (perhaps to mean the same) [It is like talking to oneself while thinking]. There are four DNA-blocks : A1, B1, A2 and B2. Ak and Bk are adjacent blocks. [Perhaps this is same as what you defined the symbols as]. A and B are ...


1

This article claims to be a new level of evidence for group selection. Its a little early to tell at this point whether the critics will be moved. They have not been in the past! sorry if this is a bit short - its late, but i'll try to come back and do more later..


1

Here is a simple proof that the probability of fixation given an infinite time is indeed p (in a finite population, otherwise there will be no fixation): Let's look at all 2N gametes in the population. Eventualy, according to the Wright-Fisher model, only one of them will be represented in the population. The probability for this gamete to be of an allele ...



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