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Point by Point to Eapen on Mumbai

1. The deal itself was signed, or brokered last year.
While negotiations started about one year ago, the deal was announced in March 2006. You also seem to gloss over the fact that it takes time to recruit for and operationalize the near-simultaneous bombing of commuter trains with military grade explosives.

2. The deal hasn't even passed Congress.
Does not matter. No one is really saying it won't pass; the debate is over how we want to word exactly what it is we want in return, with the likely outcome being broad and open-textured wording on a preferential geostrategic relationship.

3. The only germane development is the expected tacit endorsement of the deal by the G8 this week. It's still up in the air whether or not the US will be able to persuade the Nuclear Suppliers Group to lift their nuclear embargo on India without an Indian committment to the NPT.
I think my response to point (1) makes the first part of point (3) irrelevant. I think the second part of point (3) is also irrelevant: regardless of what happens with the embargo (which I don't really think is that "up in the air"), India has still displayed a desire to engage in a long term strategic parternship with the United States. If you're an AQ or AQ sympathizer and want to disincentivize favorable dispositoins to the US, India makes a great target regardless of how external elements may impede their success.

4. Al Quaeda isn't known to uniquely target India. In fact, it's more likely what's left of Al-Quaeda is probably focusing more on attacking the mainland US, US embassies, high profile govermental or economic targets situated on terrority belonging to key US allies (like the Saudis), and I'll throw Israel in there for good measure.
The same could have been said of Spain and England.

5. Terrorist attacks in India can be broadly and generally categorized into terrorism with religious motives (hindus vs. Muslims, etc) and separatist terrorism such from Kashmiri Islamic rebels or the Tamil Tigers. My knowledge of other terrorist history in this arena is shallow, so you'll excuse any omission.
The history of terrorism in India is important, but I think you're not giving due appreciation to the (recent) historical significance of the nuclear deal.

6. Specifically, Kashmiri rebels have recently been blamed for attacks of this style in the recent past. THere's no indication that there's any Quaeda involvment, though I'm sure they'd approve.

Two Kashmiri militant groups issued statements Wednesday denying responsibility for the bombings on Mumbai's commuter system that killed 183 people on Tuesday.

Lashkar-e-Tayyaba and Hezb-ul-Mujahedeen both condemned the bombings in India in separate statements released Wednesday, insisting they were not involved.
EDIT:

I want to clarify the epistemics of my position: if I had to put money on it, the scope of the operation, the use of military grade explosives and electronic timers, the simultaneity of the blasts, and the targeting of a state sympathetic to US foreign politics all point to an AQ or AQ-sympathetic/inspired attack in the vein of London or Madrid. In short: a range of possibilities makes my absolute confidence in a specific AQ link fairly temperate, but I think if you're going to put all your eggs in one basket, the choice is clear.