A sub is a method right, so I assumed its called like one.

Prototypes change how the parser interprets the syntax of a call when Perl compiles the program. It's easy to figure out which apply() function gets called when you write:

sub apply_arguments
{
    my ($item, @args) = @_;

    for my $arg (@args)
    {
        apply( $item, @args );
    }
}
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It's much more difficult to figure out which apply() method gets called when you write:

sub apply_arguments
{
    my ($self, @args) = @_;

    for my $arg (@args)
    {
        $self->apply( @args );
    }
}
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The appropriate method may not even exist at that point in the program.