Sentence:  Unfortunately – and ironically – the word ‘system' itself is used in such a wide variety of contexts within animal science, as indeed it is in virtually every domain of human activity, that confusion <WSD>reigns</WSD> about what a systems-oriented research programme actually looks like and what systems-oriented animal scientists actually do. 
Meaning of the word marked with <WSD> tags:  To be a dominant quality of a place or situation; to prevail, predominate, rule.