Its rampant use in the loose sense is clogging the literature on protein and nucleic acid sequence comparisons with muddy writing and, in some cases, muddy thinking. The word asserts a type of relationship between two or more things. Thus, amino acid or nucleotide sequences are either homologous or they are not.
Similarity is thus a quantitative property.
The first case is the most obvious offense but perhaps the least troublesome. Nonetheless, the author's ideas are likely to be clear since arguments against common ancestry are presented explicitly. The final case occurs most frequently and is the most subtle and therefore most troublesome. In this case, the two meanings of homology seem to overlap, and it is almost inevitable that the thinking of author and reader alike will be intrusively distorted as follows. Similarity is relatively straightforward to document.