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As long as the structures are actively self-organizing and self-maintaining (in the case of organisms, "alive"), they remain far from thermodynamic equilibrium with their environment.
In addition, she points out, reactions in these situations are beneficial for the receiver over an appropriate period of time (in the case of organisms, over evolutionary time).
Even in the case of organisms, we must pursue the search for mechanical explanation as far as possible, yet while still recognizing the need for an ultimate appeal to purposes.
Jablonka stresses that the benefit, or function, in the case of organisms should be understood in terms of evolution, with the focus on the evolution of the reaction system, not on the evolution of the source or the evolution of the final outcome of the reaction.
However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes.
In the case of organisms with double-stranded genomic material, the frequency of each dinucleotide must be calculated in a symmetric manner, also considering the opposite strand.
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Byrne et al.[ 12] present cases of organisms restricted to mesic habitats that were formerly most likely more widespread, but today occupy relictual areas with suitable climates.
Multiple cases exist in nature of the use of a haploid state by otherwise diploid eukaryotes, and in addendum 2, I have developed three such examples that I find particularly eloquent i.e. the cases of organisms that go through haploid stages, of the sexual chromosomes and of the endosymbiotic organelles.
VariantMetaCaller can be applied to small target regions and whole exomes as well, and it can be used in cases of organisms for which highly accurate variant call sets are not yet available, therefore it can be a viable alternative to hard filtering in cases where variant quality score recalibration cannot be used.
Nevertheless, there are many cases of organisms whose regulatory pathways have not been explicitly identified, and in those cases the real topology is usually replaced by a co-expression network, which acts as an undirected proxy for the true underlying regulatory structure.
In conclusion our work highlights the usefulness of developing predictors starting from species-specific data, so as to capture features which are characteristic of a given organism, or, such as in this case, group of organisms.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com