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Check out Understanding Evolution's general introduction to some big issues in evolution that biologists have not yet settled: The big issues.
This false dilemma appears also when considering unresolved issues in evolution or abiogenesis ("The RNA world did not resolve this problem. Thus, only creation is left as an option"; Reinikainen [2011]) or when discussing the potential moral dimensions of evolutionary theory.
Sure, there are questions and unresolved issues in evolution science.
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Of course, this is a fundamental issue in evolution of proteins that we would not attempt to solve in this paper which is dedicated to a different aspect of biochemical evolution.
Inactivation of alleles in tumor suppressor genes (TSG) is one of the important issues resulting in evolution of cancerous cells.
Topics include issues in morphological evolution and adaptation; fossil and cultural evidence for human evolution from earliest times through the Pleistocene; evolution of tool use and social behavior; modern human variation and concepts of race.
In regards to the first question, I think there may be some interesting issues in the evolution of protein requirements over the long term evolution of the biosphere, but I don't find that this raises any serious objections or alternative considerations to Higgs's conclusions – except perhaps in one area.
Achieving an accepted phylogeny had been one of the most contentious issues in arthropod evolution for many decades.
The way network resources, primarily bandwidth, is shared, is one of the key issues in this evolution.
Indeed, recent studies have applied evolutionary game theory to key issues in the evolution of energy metabolism.
This video/multimedia case can be used to discuss key issues in the evolution of many American cities, such as white flight, institutional racism and deindustrialization.
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