Tag Info

Hot answers tagged

44

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). ...


17

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 ...


13

Welcome to Biology.SE. Am I remembering this incorrectly? Yes, you're remembering well. I think you're talking about slime molds. You'll find more information on the wiki page Is this the video you saw? These images are pretty cool. Is this even possible? Yes (given that it exists). There is no way to correctly answer this question as it really ...


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 ...


12

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 ...


10

Population dynamics occupies a whole subset of mathematical biology. Perhaps the most pragmatic uses for modelling population dynamics come from the fields of epidemiology for modelling disease infection and transmission through a population (one such article), or ecology modelling things like forestation, fishing dynamics, predator-prey relationships (an ...


8

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. ...


8

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 ...


7

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 ...


7

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 ...


7

kmm's answer is great and complete; 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 ...


6

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 ...


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

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 ...


6

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 ...


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 ...


6

Parallel DNA helix can exist and this has been observed experimentally. However these structures are stabilized by Hoogsteen type base pairing [1,2] and not the usual Watson-Crick type pairing because the parallel conformation does not allow the latter (See the figure below). This elongates the hydrogen bonds and also causes a loss of one hydrogen bond ...


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 ...


5

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 ...


5

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 ...


5

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 ...


5

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 ...


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

These kind of equations (the Michaelis-Menten [MM] like term) denote saturation kinetics. The basic mechanistic assumption behind saturation kinetics is this: A rate (of lets say product formation) is dependent on the concentration of a molecule such that the rate increases linearly with increase in the concentration of the molecule. Example 1: Substrate ...


5

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 ...


4

Relating to your last comment on random fluctuations in survival, a recent theoretical paper by Lee et al. 2011 studies the effect of mating systems on demographic stochasticity in small population. No empirical data there though. Their main conclusion is that polygyny (in relation with sex ratio) can lead to high demographic variance, therefore lowering ...


4

What you are describing usually falls under the category of computational biology or just mathematical biology. Unfortunately, the biggest part of this field is bioinformatics, or the application of statistical and/or dynamical programming techniques to sequence data. You exclude this in your question, and I would agree with you that it is a "boring" topic ...


4

This is derived from studying how heterozygosity changes over time. The standard equation for change in heterozygosity ($H$) with constant population size ($N$) is: $H_t = \left(1 - \frac{1}{2N}\right)^tH_0$ When $N$ varies between generations you use the product of this formula: $H_t = \left(1 - \frac{1}{2N_0}\right)\left(1 - ...


4

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 ...



Only top voted, non community-wiki answers of a minimum length are eligible