I would also add some kind of white-glove treatment to prevent a scrutineer from hiding a pencil lead or pen tip under his fingernails. Although the requirement to write out the candidate's name in full provides some resistance against this sort of attack.
Probably the biggest risk is complacency. What might seem beautiful in its tradition and ritual during the first ballot could easily become cumbersome and annoying after the twentieth ballot, and there will be a temptation to cut corners to save time. If the Cardinals do that, the election process becomes more vulnerable.
A 1996 change in the process lets the cardinals go back and forth from the chapel to their dorm rooms, instead of being locked in the chapel the whole time, as was done previously. This makes the process slightly less secure but a lot more comfortable.
Of course, one of the infirmarii could do what he wanted when transcribing the vote of an infirm cardinal. There's no way to prevent that. If the infirm cardinal were concerned about that but not privacy, he could ask all three infirmarii to witness the ballot.
There are also enormous social -- religious, actually -- disincentives to hacking the vote. The election takes place in a chapel and at an altar. The cardinals swear an oath as they are casting their ballot -- further discouragement. The chalice and paten are the implements used to celebrate the Eucharist, the holiest act of the Catholic Church. And the scrutineers are explicitly exhorted not to form any sort of cabal or make any plans to sway the election, under pain of excommunication.
The other major security risk in the process is eavesdropping from the outside world. The election is supposed to be a completely closed process, with nothing communicated to the world except a winner. In today's high-tech world, this is very difficult. The rules explicitly state that the chapel is to be checked for recording and transmission devices "with the help of trustworthy individuals of proven technical ability." That was a lot easier in 2005 than it will be in 2013.
What are the lessons here?
First, open systems conducted within a known group make voting fraud much harder. Every step of the election process is observed by everyone, and everyone knows everyone, which makes it harder for someone to get away with anything.
Second, small and simple elections are easier to secure. This kind of process works to elect a pope or a club president, but quickly becomes unwieldy for a large-scale election. The only way manual systems could work for a larger group would be through a pyramid-like mechanism, with small groups reporting their manually obtained results up the chain to more central tabulating authorities.
And third: When an election process is left to develop over the course of a couple of thousand years, you end up with something surprisingly good.
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