It is the world’s largest Muslim country but remains for the most part secular. It is home to the eighteenth largest economy on the globe but more than sixteen percent of the population lives on less than $2 per day. Indonesia has long been considered the linchpin for Southeast Asia and, indeed, serves as a fascinating case study for which myriad domestic phenomena can be explored:  macroeconomic policy, the role of religion, and the nexus between political control and the military. In the seventh episode of the 2012 Great Decision series, produced by the Foreign Policy Association, Indonesia’s role in the region and the world, as well as its relationship with the United States, is examined in such frameworks. FPA readers can purchase a copy of the eight episode DVD and briefing book at the Great Decisions TV webpage.

The two panelists – Walter Lohman, the Director of The Heritage Foundation’s Asian Studies Center, and Sadanand Dhume, a columnist for the Wall Street Journal – start with an historical overview beginning in the Cold War era to properly contextualize Indonesia’s modern trajectory.

Fearful of a communist wave which threatened to sweep Southeast Asia into Moscow’s orbit, U.S. policymakers in the Richard Nixon administration were quick to align themselves with Suharto, a zealous anti-communist Major General who had helped to overthrow the country’s previous military ruler in 1967. As Lohman posits, Washington’s support for Suharto was the lesser of two evils.

Never one to shy away from befriending some of the world's worst dictators, President Richard Nixon hosts Suharto in the Oval Office in 1969. Photo: ETAN

Despite a lack of political and civil rights under Suharto, Dhume argues that the dictator showed a knack for organization and, as a result, Indonesia underwent a period of extraordinary economic growth (abetted by millions of dollars in aid from Washington) while also enjoying some measure of political stability. Dhume is quite cavalier, however, in his dismissal of Suharto’s human rights record, saying only that there were “abuses of course,” before moving on to another point.

After the overthrow of Sukarno, the country’s previous autocrat, Suharto went on a rampage against his political opponents, especially Communists, which resulted in a bloodbath that rivaled Stalin’s endeavors in terms of sheer brutality. In December 1975, Indonesia invaded and occupied East Timor, causing untold misery and close to 100,000 deaths over the course of the following quarter century. Moreover, the Suharto regime’s behavior in West Papua has been called genocide by the Yale Law School. Yes, there were abuses, of course.

Suharto’s downfall came against a backdrop of the Asian financial crisis in 1997. Indonesia’s population could tolerate Suharto’s corruption and nepotism as long as the economy continued to hum along. However, the financial collapse which hit the country was not only an economic calamity but also served as a social and political awakening as well.

Indonesians go to the polls in 1999, the culmination of a remarkably quick transition to democracy. Photo: China Daily

The elections held in 1999 were, by all accounts, free and fair. Such a reality was met with surprise by most observers who have noted the chaotic nature of quick democratic transitions. One need only look to Egypt today to find an appropriate juxtaposition. With a litany of actors – opposition figures, military personnel, and remnants from the old regime — all clamoring for a voice at the table, one should expect a rocky road. In Indonesia, there were a fair share of bumps in that road, especially between 1998 and 2002, but the end product can be held up as a model to follow for other countries undergoing the trials and tribulations of democratization.

Indonesia’s transition from autocratic rule to democracy is almost as unique as the country itself. Consisting of more than 17,000 islands, the Great Decisions panel brings up the question as to how Indonesia has maintained its territorial integrity through the years. With the exceptions of East Timor, which gained independence in 2002, and the continued struggle by separatists in West Papua, Indonesia has retained sovereignty over its whole.

Part of that was due to the iron fisted rule of Suharto, but another part is due to the nation’s religious freedom. While 88 percent of the country is Muslim, there are major areas that are home to religious minorities. Bali, for example, is largely Hindu, while Sumatra is Christian. These groups have never been persecuted for their beliefs and that has gone a long way preventing the type of schisms that have popped up in other areas of the world which have divaricating degrees of religious tension. A good contemporary example in the news lately is Nigeria, where sectarian fighting in the country’s north threatens to tear the nation apart.

In terms of democratization and minority rights, Dhume suggests that Indonesia can be an example for countries involved in the Arab Spring. This is so not just because of the mutual connection to Islam, but because Indonesia has proven that such transitions can be successfully implemented.

The United States, for its part, has maintained a very close partnership with Jakarta, even after he Suharto years. The two countries participate in various military exercises together, and have cooperated fully in the apprehension of several well-known members of Jemaah Islamiyah, a militant Islamic organization operating in Southeast Asia.  Washington values its relationship with countries like Indonesia because of the non-political role of Islam and because of its ability, in the 21^stcentury at least, to curtail the influence of the military in the political process.

President Barack Obama, seen here meeting with Indonesia President Susilo Bambang Yudhoyono in 2010, spent part of his childhood in Indonesia. Photo: Corbis Images

President Barack Obama has a personal connection to Indonesia, having spent four years of his childhood living there. He has also made two state trips to the country as President in only his first term. Ties between the two countries appear to be very strong at the moment – a reality which Indonesian President Susilo Bambang Yudhoyono has boasted of on numerous occasions – and with Indonesia’s GDP having increased sevenfold just over the last fifteen years, Jakarta is poised to be a regional powerbroker and a significant international player in the years to come.

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Welcome to Indonesia.

On December 1st, 1961, the Dutch flag which had flown over the peninsula of West Papua for more than 130 years was taken down, replaced by the “Morning Star” flag which signified the new nation’s break from colonialism. By the end of the decade, Indonesia had forcefully annexed West Papua (also known as West Irian at the time) with tacit support from the United States. Fifty years later — an anniversary which was marked yesterday — National Flag Day is remembered by the West Papua independence movement as resistance leaders and human rights advocates recall the brutal military takeover of the country by Suharto’s Indonesia as well as the hope which the “Morning Star” flag still epitomizes today.

Indonesia was granted independence from the Netherlands in 1949, but the Dutch maintained control over West New Guinea. US-sponsored mediation between the former colonizer and colonized led to Indonesia assuming full control of the region by the end of 1962 on the condition that Jakarta would allow a local vote on the issue of self-determination under United Nations supervision. What followed was a decade long crackdown on any manifestations of political opposition and dissent by Suharto. The “Act of Free Choice,” held under dubious conditions in 1969 in which Jakarta handpicked elders of the Papuan community to agree to become part of Indonesia, was supported and recognized by the West and the UN. The ”community elders” have been widely quoted since then that they were forced to vote at gunpoint to be part of Indonesia.

Indonesia’s crimes in Timor-Leste during the Cold War era until the end of the 20th century are well documented. But Indonesia’s behavior in West Papua over the past half century has been underreported in mainstream news outlets. During this timeline, approximately 100,000 Papuans were killed; almost ten percent of the population. The Yale Law School has labeled it genocide. Evidence of Indonesia’s repression is revealed in the exploitation of West Papua’s land and resources, as well as scores of accounts of rape, torture, and extrajudicial killings.

The separatist Free Papua Movement (OPM) was set up in the mid-1960s in response and began waging a guerrilla struggle against the Indonesian military. The erosion of Papuan culture and tradition was the raison d’etre for leaders of the movement, and an armed struggle has persisted on and off in the decades since. In the 1980s, Jakarta launched Operation Clean Sweep, which targeted family members of OPM fighters in an effort to defeat the movement. Electric shocks, public rapes, and death by means of bayonets were just some of the methods employed by Indonesian soldiers.

In Jakarta’s attempt to exploit the region’s wealth of gold, copper and timber, West Papuan villagers were routinely uprooted from their homes without any compensation and without the required labor skills to survive such a transition. Forced labor of many indigenous tribes in West Papua was also common practice; resistance was typically met with torture. Moreover, West Papua has long been a victim of socioeconomic neglect: access to education is minimal, 41.8% of the population live below the poverty line, and the prevalence of HIV/AIDS has exploded.

Today, it is a crime to fly the “Morning Star” flag, as the world found out through the infamous incarceration of activist Yusak Pakage, a prisoner of conscience according to leading human rights groups. The OPM have no plans to abandon the ceremony on the 50th anniversary of National Flag day on the first of December, 2011. Rallies and demonstrations took place in West Papua, and Jakarta responded by directing additional security service personnel to the region.

West Papua was given special autonomy status in 2001, but human rights abuses, committed by Indonesian paramilitary forces, persist to this day. The West has gradually begun to apply additional pressure on Jakarta to ease its treatment of civilians in West Papua, but it has not nearly matched the effort that observes have seen exerted on governments in other, well-publicized areas of the world.

Indonesia needs the West as much as the West needs Indonesia. It is a complex area of US foreign policy, but the success of such symbiotic relationships is predicated on transparent dialogue and communication between the two parties. The 50th anniversary of National Flag Day should be used by Washington and other Western governments as a way of highlighting the situation of the West Papuans so as to bring a certain level of justice to this continued struggle, as well as an attempt to modify Jakarta’s Papuan policy even further.