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Suppose you have two identical copies of the same, coding nucleotide sequence (e.g. two copies of BCL2 - a random gene I found on Wikipedia).
Could you say that these are two genes (i.e. the name "gene" refers to a specific, physical sequence, and where there are two of them, you have two genes, even if identical)? Or just two molecules of one gene (in the same way that when you have two molecules of carbon dioxide, you can't say that they are two carbon dioxides)?
'just two molecules of one gene'.
They are the same gene. Gene is more of an abstract concept. We say for example that humans have ~ 20,000 protein-coding genes. It does not mean that we have only 20,000 molecules, one for each gene. We have many more molecules of course. What we mean is that we have 20,000 different entities, each coding for a specific type of protein. If you have two molecules of a sequence in a tube, it becomes questionable whether these sequences can be thought of as genes. I would say that those sequences lose their 'genicity' or their property of being genes because they are not coding for anything in a tube. They lack the cellular machinery that makes them code for something. I would just say you have 2 nucleotide sequences of the gene BCL2 but not that you have 2 copies of the gene BCL2. It's maybe just a personal difference I see though.
A gene is more a functional unit in the genome. As such if you have, say, 5 sequences of the same gene, you will say that you have 5 copies of this gene but you won't say that you have 5 genes. If you say that you have 5 genes, then we would think that you refer to 5 different loci (locus = position in the genome).
Note that if you are not familiar with the term allele, then you will want to check it out. An allele is a variant of a gene. Again, an allele is more the information in the sequence than the sequence itself (a gene is typically a coding region). Therefore, if you say that at gene BCL2, there are 4 alleles in the populations, that means that there are 4 possible variants in the population, not that the whole population is made of only 4 physical sequences of this gene.
