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Most obviously, it will fail when the environment that is being adapted to consists of a competing, or predator, or prey, or host or parasite lineage that is itself undergoing a process of counter-adaptation.
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This does not necessarily mean that these methods will fail when their assumptions are incorrect, but it suggests that it is important to explore a range of different objectives for reconciling gene trees.
From an engineering standpoint, a structure will fail when the loads applied to it exceed its strength.
Your description will fail when your reader doesn't know who Tom Cruise is.
An obvious disadvantage with this approach is that locating will fail when the mark cannot be seen.
Every key facet required for business success will fail when sleep becomes short within an organisation.
Linear dimensionality reduction will fail when the output space is not well approximated by a linear subspace of the ambient space in which it lies.
Since concrete is poor in tension, a beam without any form of reinforcement will fail when subjected to a relatively small tensile load.
They know 90% of their investments will fail when they go to market, and that's acceptable.
More organizations will be created, and fewer organizations will fail, when the legitimation of the form is high and competition is weak.
Many of Algeria's 1.5m students will fail, when they graduate, to work in the field for which they have been trained.
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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