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I disagree that this is just a protocol or convention from another language. There is a lot more to this issue.
The heart of this question is what your model of OO programming is. The ref trick makes Perl halfway towards being prototype based, but not really. Avoiding it allows you to have a model closer to Smalltalk's, which works much better in Perl. Given that I prefer Smalltalk's model, I am inclined towards merlyn's position. But given that the ref trick can't make the prototype approach work, I think that he is objectively right.
(Those who don't know what I am talking about when I talk about prototypes should read the explanation I gave at A Cat's eye view of OO.)
If you want to take a prototype approach in Perl, you can. Do it with BikeNomad's Class::Prototyped and have it work right. Don't do it with a half-way hack that allows you to maintain a bad mental model of your code that won't really work if you push it.
Furthermore merlyn's accusation that it is typically cargo-cult programming is definitely on target. Take 10 random people who regularly use the ref meme in their constructors. Of them at least 8 have never given any serious thought to the question of why they would want to write code that way. They have no clear thoughts on it at all. They have just seen the construct, use it because they have seen it, but they have no strong thoughts on what the reason is. That is exactly what cargo-cult programming is. The blind repetition of programming patterns that you have not thought about and do not understand.
And about the two other examples you gave. Steve McConnell was circumspect about saying how bad Hungarian Notation is in his classic Code Complete, but what he said there about why it is bad is exactly correct. And it was correct coming from someone who had (among other things) done VB programming for Microsoft in the 90's. Secondly nobody programmed in C in the 1960's. It wasn't invented until the 70's. Even if it were, the use of context in Perl is something a C programmer should have no opinion on since the concept doesn't exist in C. By contrast the use of objects in Perl is something which a user of another OO language reasonably can have opinions on in Perl because it exists both places. Their opinions might be wrong for Perl, but they at least have an experience base which is somewhat relevant.
In reply to Re (tilly) 2: Paradigm Shift - Dual Use Constructors