For example, the $taxon object (being a representation of our concept of a "species") with the name 'Homo sapiens' could be instantiated at some point, and subsequently a $sequence object containing a human DNA sequence could be created. I want to create a link between the sequence and the taxon. In fact, I might want to link many sequences to that one taxon (say, a set of genes sequenced from a human subject), and link many nodes (from different trees) to that one taxon. Simply put: there's a one-to-many relationship from taxon to nodes and sequences, and a one-to-one relationship from node to taxon, and from sequence to taxon.

The end result should be that I can do things like:

my @sequences = $taxon->get_sequences;
my @nodes     = $taxon->get_nodes;
my $taxon     = $node->get_taxon;
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I have so far used a design where the nodes and sequences have a set_taxon method (where the ref to the taxon is stored as a field in the object), and the taxon objects have set_nodes and set_sequences methods (also with fields for those, directly in the object). This strikes me as bug prone, because all the relationships automatically have to be bidirectional.

The quick fix is to say that whoever is called to set_whatever needs to check whether or not the link in the other direction exists, and make one if not. Then, you have to prevent these calls from bouncing back and forth, and pretty soon you're in if/elsif/elsif... territory.