Entropy in the Tangled Nature Model of Evolution

Roach, Ty N. F.; Nulton, James; Sibani, Paolo; Rohwer, Forest; Salamon, Peter

doi:10.3390/e19050192

Cited by 21 publications

(10 citation statements)

References 22 publications

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“…However, in general, living systems tend to maximize power over short time scales and when resources are high, and tend to minimize dissipation over longer timescales or when resources are low. This can be seen in the strategies employed at several biological scales, including organismal development, ecological succession, and long-term evolution [142]. Better understanding the roles of compensated heat and waste heat in biology will provide novel insight into the underlying physical mechanisms driving biological processes at multiple temporal and spatial scales.…”

Section: Resultsmentioning

confidence: 99%

Application of Finite-Time and Control Thermodynamics to Biological Processes at Multiple Scales

Roach

Salamon

Nulton

et al. 2018

Journal of Non-Equilibrium Thermodynamics

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An overall synthesis of biology and non-equilibrium thermodynamics remains a challenge at the interface between the physical and life sciences. Herein, theorems from finite-time and control thermodynamics are applied to biological processes to indicate which biological strategies will succeed over different time scales. In general, living systems maximize power at the expense of efficiency during the early stages of their development while proceeding at slower rates to maximize efficiency over longer time scales. The exact combination of yield and power depends upon the constraints on the system, the degrees of freedom in question, and the time scales of the processes. It is emphasized that biological processes are not driven by entropy production but, rather, by informed exergy flow. The entropy production is the generalized friction that is minimized insofar as the constraints allow. Theorems concerning thermodynamic path length and entropy production show that there is a direct tradeoff between the efficiency of a process and the process rate. To quantify this tradeoff, the concepts of compensated heat and waste heat are introduced. Compensated heat is the exergy dissipated, which is necessary for a process to satisfy constraints. Conversely, waste heat is exergy that is dissipated as heat, but does not provide a compensatory increase in rate or other improvement. We hypothesize that it is waste heat that is minimized through natural selection. This can be seen in the strategies employed at several temporal and spatial scales, including organismal development, ecological succession, and long-term evolution. Better understanding the roles of compensated heat and waste heat in biological processes will provide novel insight into the underlying thermodynamic mechanisms involved in metabolism, ecology, and evolution.

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Section: Resultsmentioning

confidence: 99%

Application of Finite-Time and Control Thermodynamics to Biological Processes at Multiple Scales

Roach

Salamon

Nulton

et al. 2018

Journal of Non-Equilibrium Thermodynamics

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“…The Shannon entropy (SE) mesures information-entropy of a Bernoulli process with probability p of the two outcomes (0/1) 45 – 47 . It is defined as where and ; here l is length of the binary string and k is the number of 1’s in the binary string of length l .…”

Section: Methodsmentioning

confidence: 99%

Analysis of Purines and Pyrimidines distribution over miRNAs of Human, Gorilla, Chimpanzee, Mouse and Rat

Das

Choudhury

Chaudhuri³

et al. 2018

Sci Rep

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Meaningful words in English need vowels to break up the sounds that consonants make. The Nature has encoded her messages in RNA molecules using only four alphabets A, U, C and G in which the nine member double-ring bases (adenine (A) and Guanine (G)) are purines, while the six member single-ring bases (cytosine (C) and uracil (U)) are pyrimidines. Four bases A, U, C and G of RNA sequences are divided into three kinds of classifications according to their chemical properties. One of the three classifications, the purine-pyrimidine class is important. In understanding the distribution (organization) of purines and pyrimidines over some of the non-coding RNAs, all miRNAs of the three species (human, gorilla and chimpanzee) of Hominidae family and two species (mouse and rat) from of Muridae family are considered. The distribution of purines and pyrimidines over miRNA shows deviation from randomness. Based on the quantitative metrics (fractal dimension, Hurst exponent, Hamming distance, distance pattern of purine-pyrimidine, density distribution of purine-pyrimidine and Shannon entropy) five different clusters have been made for the five species. We have observed some couple of results including the closeness of different clusters among the five species.

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“…The Shannon entropy (SE) is defined as the entropy of a Bernoulli process with probability p of one of two values [40,41,42]. It is defined as…”

Section: Shannon Entropy Of Mirnasmentioning

confidence: 99%

Distribution of Purines and Pyrimidines over miRNAs of Human, Gorilla and Chimpanzee

Das

Choudhury

Chaudhuri³

et al. 2017

Preprint

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Meaningful words in English need vowels to break up the sounds that consonants make. The Nature has encoded her messages in RNA molecules using only four alphabets A, U, C and G in which the nine member double-ring bases (adenine (A) and Guanine (G)) are purines, while the six member single-ring bases (cytosine (C) and uracil (U)) are pyrimidines. Four bases A, U, C and G of RNA sequences are divided into three kinds of classifications according to their chemical properties. One of the three classifications, the purine-pyrimidine class is important. In understanding the distribution (organization) of purines and pyrimidines over some of the non-coding regions of RNA, all miRNAs from three species of Family Hominidae (namely human, gorilla and chimpanzee) are considered. The distribution of purines and pyrimidines over miRNA shows deviation from randomness. Based on the quantitative metrics (fractal dimension, Hurst exponent, Hamming distance, distance pattern of purine-pyrimidine, purine-pyrimidine frequency distribution and Shannon entropy) five different clusters have been made. It is identified that there exists only one miRNA in human hsa-miR-6124 which is purely made of purine bases only.

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Entropy in the Tangled Nature Model of Evolution

Cited by 21 publications

References 22 publications

Application of Finite-Time and Control Thermodynamics to Biological Processes at Multiple Scales

Application of Finite-Time and Control Thermodynamics to Biological Processes at Multiple Scales

Analysis of Purines and Pyrimidines distribution over miRNAs of Human, Gorilla, Chimpanzee, Mouse and Rat

Distribution of Purines and Pyrimidines over miRNAs of Human, Gorilla and Chimpanzee

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