One of Indonesia's achievements in the last eight years has been to re-civilise their political institutions after Suharto militarised them to the point of permanent corruption. Many of the ills in the Indonesian system, and future challenges involve flushing the mix of military and civil responsibilities in the Indonesian political system.

Indonesia's military under Suharto had seats in their main legislative body, the Majelis Permusyawaratan Rakyat ; occupying twenty percent of the seats. The Indonesian democrats, those committed to good governance and civil control of government, finally flushed the military from their unicameral legislative body in October 2004 . If anything they managed to speed up the democratic reform process as the initial agreement was for no military parliamentary seats by 2007.

The TNI also maintains a regional and local structure which is a left over from their days when they controlled civil order. At the TNI's height it comprised four hundred thousand soldiers, of which two hundred thousand were military police devoted to civil order.

It is hard to imagine that Indonesia did not have a police force until recently. In 1964 the police force was subsumed into the military at Sukarno's demand. It remained under military control until 1999 when it was separated from the TNI, even though it remains under the defence minister's control it is now part of the Executive, rather than the military.

The TNI is well known, even now, for abusing its power by trying to control separatist groups; East Timor, Aceh and West Papua are examples of this. While this may have been par for the course under Suharto, it is no longer acceptable under a civil government.

The Aceh treaty was an under-reported success. It was an incident where the civil government asserted their control over the TNI, wresting political power from them, in an area where they were allowed open-slather under Suharto.

The Munir Said Thalib trial is another under-reported example of the civil government asserting control, this time over the BIN and Indonesian intelligence community.

The Indonesian government was stamping their foot down over what was nothing more than the BIN acting as mavericks and executing a civilian.

The recent nationalist stance by Yudhoyono over the West Papua refugees was discouraging. The disturbances are undoubtedly being caused by the TNI acting outside of parliamentary and presidential control.

I don't consider nationalism a valid ideology. It is a political device, designed to reflexively collapse popular support to the central government.

That Yudhoyono used nationalism and Konfrontasi politics, such as recalling an ambassador, suggests that he is politically weak at home and the TNI have the upper hand in West Papua.

This is not good for Indonesia, Indonesian democracy and Australia. Both countries are dependant on stable and secure relations for not on their own, but their neighbours, prosperity.

Focusing on the ills of the Suharto regime are informative on how not to run a government. I read this morning that President Bush is considering expanding the National Guard's (state militia) presence in border control activities.

Apart from them not being the President's to command, they have to be requested from the states, the existing National Guard are deployed on emergency powers in Arizona and New Mexico.

But the national security state is another permutation of the state of exception going from exception to permanence. If the National Guard is being deployed then it is likely that a once civil responsibility will become militarised.

Like Indonesia's police were.

The American CIA is a civil agency that is part of the executive. Recently President Bush nominated a uniformed officer to head the civil agency. This is another example of the militarising of the civil government structures.

As Indonesian history shows us, as does their recent struggles to re-establish liberal democracy, mixing the military and civil has negative effects.

For liberty's sake, they are best kept entirely separate.