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ref: -2020 tags: evolution neutral drift networks random walk entropy population date: 04-08-2020 00:48 gmt revision:0 [head]

Localization of neutral evolution: selection for mutational robustness and the maximal entropy random walk

  • The take-away of the paper is that, with larger populations, random mutation and recombination make areas of the graph that take several steps to get to (in the figure, this is Maynard Smith's four-letter mutation word game) are less likely to be visited with a larger population.
  • This is because the recombination serves to make the population adhere more closely to the 'giant' mode. In Maynard's game, this is 2268 words of 2405 meaningful words that can be reached by successive letter changes.
  • The author extends it to van Nimwegen's 1999 paper / RNA genotype-secondary structure. It's not as bad as Maynard's game, but still has much lower graph-theoretic entropy than the actual population.
    • He suggests if the entropic size of the giant component is much smaller than it's dictionary size, then populations are likely to be trapped there.

  • Interesting, but I'd prefer to have an expert peer-review it first :)

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ref: -0 tags: co2 capture entropy carbon dioxide date: 09-22-2019 00:46 gmt revision:1 [0] [head]

How much energy is thermodynamically required to concentrate CO 2CO_2 from one liter of air?

CO 2CO_2 concentration is 400ppm, or 0.4%. 1l of air is 1/22.4 or 44mMol. From wikipedia, the entropy of mixing is:

Δ mixS=nR(x 1ln(x 1)+x 2ln(x 2)) \Delta_{mix} S = n R (x_1 ln(x_1) + x_2 ln(x_2)) where x 1x_1 and x 2x_2 are the fraction of air and CO 2CO_2 (0.996 and 0.004)

This works out to 9.5e3J/K9.5e-3 J/K . At STP, 300K, this means you need only about 2.9J2.9 J to extract the carbon dioxide.

A car driving 1 km emits about 150g carbon dioxide. This is 3.4 moles, which will diffuse into 852 moles of air, or 19e3 liters of air (19 cubic meters). To pull this back out of the air then you'd need at minimum 55.3 kJ.

This is not much at all -- a car produces 100kW mechanical power, or 100kJ every second, and presumably it takes a minute to drive that 1km. But such perfectly efficient purification is not possible.

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ref: -0 tags: entropy life proteonomics transcription factors date: 07-08-2011 22:42 gmt revision:0 [head]

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes -- read the article. These are my disordered, mesothermophylic notes.

  • Low and high temperature prokaryotes seem to have less protein disorder (as estimated by amino acid content, mostly, not actual structure) called IDR/IDP (intrinsically disordered regions or proteins).
  • IDR / IDPs seem essential in certain protein functions, such as transcription factors and ribosomal proteins.
  • hyperthermophyles have low genomic complexity and low protein disorder, possibly to combat the high disorder of their environment.
  • "life appears to be incompatible with less than about 1.5% disorder ". I would say that this is a rather conservative threshold.
  • transcription factors: "disorder is correlated with the number of genes they regulate, which suggests that their disorder is directly linked with functional complexity of the organism"
  • Transcription factor disorder is higher in psychrophiles (low temp) than hyperthermophiles, even though both show decreased genome size. Furthermore, disordered regions may confer temperature robustness at 40-50C as well as at low temperatures.
  • "...there is many evidence in the literature that structural disorder and complexity are correlated, both at the level of individual proteins, where IDP functions correlate with signaling and regulation, and whole genomes, where the frequency of disorder increases with increasing complexity of the organism [24], [25], [41], [52]. Thus, evolutionary changes (point mutations, deletions of regions, silencing of genes, etc…) that reduce disorder will tend to strip the organism of functions that increase its complexity, and leave functions that are required for its basic, non-regulated existence. In this sense, reduction in disorder is not a side-effect of selection for reduced complexity, rather the mechanism of this evolutionary drive."

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ref: -0 tags: conjecture entropy simulation date: 03-25-2011 18:16 gmt revision:0 [head]

Conjecture: the entropic cost of simulating a system (complex evolved or not) in a system (e.g. machine) versus physical reality is proportional to the information content of original system * energy per bit of simulation * time to simulate / KL divergence between simulation and reality, where information content KL divergence are calculated within the space of measured dimensions.

Am I missing terms? Or rather: what terms am I missing? :-)

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ref: bookmark-0 tags: information entropy bit rate matlab code date: 0-0-2006 0:0 revision:0 [head]


  • concise, well documented, useful.
  • number of bins = length of vector ^ (1/3).
  • information = sum(log (bincounts / prior) * bincounts) -- this is just the divergence, same as I do it.

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ref: bookmark-0 tags: machine_learning classification entropy information date: 0-0-2006 0:0 revision:0 [head]

http://iridia.ulb.ac.be/~lazy/ -- Lazy Learning.