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The embattled regime of Bashar al-Assad has presented the conflict over the past 17 months as the defence of a secular state in the face of an extreme Sunni-supremacist onslaught backed by Gulf Arabs and the West. Yet the core of the regime is overwhelmingly drawn from his Alawite sect, and the ferocity of its actions reflects the fears of a tribal sectarian minority with its back to the wall.

This contradiction, between a regime which proclaims to be secular and its reliance on members of a sect that comprises only 12 per cent of the population, has grown more acute as the uprising has gathered strength. The regime has ratcheted up the violence of its response, with the cleansing by the regime militia, the shabbiha, of Sunni neighbourhoods in the mixed city of Homs and the massacres of Sunni villagers in three rural areas on the fringe of the Alawite heartlands in the hills rising up from the Mediterranean coast.

These massacres have prompted speculation that the Alawites are preparing to retreat to their ancestral homeland for a last stand to avoid the vengeance of the Sunni majority. But is this retreat to the mountains a real possibility for the Alawites, some of whom have enjoyed wealth and power over the past 40 years when they dominated the state? Or is it more likely that Alawite unity will fracture under pressure of the uprising and some generals and tribal leaders will turn on the Assad clan and its closest allies?

Alawites with long memories will see some echoes from the past in their current predicament. Since the breakaway Shia sect emerged in what is now Iraq in the 9th Century it has frequently been engaged in battles for survival against a hostile Sunni orthodoxy. The sect's founder, Mohammed ibn Nusayr, distinguished himself from the mainstream Shia by venerating Ali ibn Abi Talib, son-in-law of the Prophet Muhammad and the first imam of the Shia branch of Islam, as a deity. As the Abbasid empire fractured, members of the sect fled, finding refuge eventually in the rugged mountains of northwest Syria.

Leon Goldsmith, a researcher into the sect, argues that its marginalization over ten centuries has been a source of weakness and strength: it has kept the Alawites back politically and economically - until the Assad era - but it has also fostered a strong sense of communal cohesion.

A defining moment of Alawite history was a fatwa issued by Ibn Taymiyya, a Sunni jurist, in 1318 after the suppression of an Alawite uprising by the Mamluk authorities, who wanted to spread Sunni orthodoxy throughout their realm. The fatwa was in the form of an answer to a rather loaded question, asking what the correct view should be towards the Alawites in light of their dubious practices, including the drinking of wine, a belief in the transmigration of souls and the deification of Ali. Ibn Taymiyya pronounced that the sect was more heretical than the Jews or the Christians and that their harm to the Muslim community was worse than that of the Crusaders and Mongols, owing to their false claim to be followers of Islam.

The Ibn Taymiyya stigma lasts to this day, despite more recent affirmations of the Alawites standing as legitimate adherents of Islam. One of the most significant was a ruling by Hajj Amin al- Husseini, the Mufti of Jerusalem, in 1936, which paved the way for the Alawites to join the unified Syrian state established under the French mandate-they had previously held autonomous status.

Under the French, the Alawites started to play an important part in the Syrian armed forces, and this trend continued during the early years of independence.

Advancement through the military and involvement in Arab nationalist political activity created the platform for ambitious Alawites to make their bid for power in the mid-1960s. Three years after the Baath party took power in 1963, an Alawite faction assumed control behind the scenes.

Hafez al-Assad, father of the current president, seized control in 1970. The Alawite ascendancy did not appear to have followed any grand design, but arose from the strong bonds between members of a rural and historically marginalized minority that had seen opportunities open up. The rise of the Alawites soon met opposition from sections of the Sunni majority. In 1976, after a crackdown in Hama by forces led by the Rifaat al-Assad, the then president's younger brother, the Muslim Brotherhood launched a revolt, aimed at ending the rule of the ‘heretic' minority.

This rising was brutally crushed, culminating in the assault on Hama in 1982 in which an estimated 20,000 people were killed. Hafez al-Assad subsequently co-opted Sunni merchants in Damascus and Aleppo, but strengthened the Alawite hold on the military and intelligence services. Alawites now comprise 80 per cent of officers in the Syrian armed forces, including more than 90 per cent of the generals.

The Muslim Brotherhood and the more extreme Salafists are once more pitted against the Assad regime in the current uprising, but there are significant differences between the revolt of the 1970s and now. Today, the religious-based anti-Alawite theme is subsidiary to the main thrust of opposition to a corrupt dictatorship.

The uprising began in peaceful mass protest, only taking on military aspects after the regime had killed hundreds of unarmed civilians. The video streams from there have plenty of anti-Alawite diatribes, but this is by no means the dominant discourse.

The cohesion of tribal groups tends to dissipate once they become softened by urban power. Will this happen to the Assad regime? The Alawites have suffered internal discord in the past, most dramatically with Rifaat al-Assad's abortive effort to supplant his ailing brother Hafez in 1983-84. Rifaat failed because he underestimated the loyalty of the Alawites to their leader. There was also a backlash against Bashar al-Assad among some Alawite tribal leaders when Ghazi Kenaan, who had racked up 20 years as Syria's intelligence chief in Lebanon, was declared to have killed himself in 2005; his brother, Ali, also succumbed to a similar case of suspected ‘assisted suicide' the next year. The care that the Kenaan brothers had taken to look after their people back in the Alawite mountains was contrasted unfavourably with the behaviour of Bashar, who seemed to be more concerned with opening up business opportunities for his close circle in the metropolis.

There are no visible cracks in the Assad regime leadership, but there has been a division of labour, with Bashar's younger brother, Maher, perceived as playing the leadership role in military affairs (much like Rifaat's role vis-à-vis Hafez), and the shabbiha militias re-emerging as a key force in fighting the Alawite cause.

The shabbiha first appeared in the 1970s as an Assad clan mafia running smuggling operations. The flourishing of private business during the late 2000s was portrayed by some as an elevation of the Assad mafia, headed by the president's cousin, Rami Makhlouf, to a higher plane, with the more thuggish elements kept in check.

Over the past 18 months the shabbiha have returned with a vengeance, and have been blamed for many of the most gruesome sectarian massacres. Their actions raise the question of whether Alawites retaining close ties to their ancestral heartlands are preparing for a retreat to these areas as a line of defence against a resurgent Sunni state seeking bloody retribution. The sheer weight of numbers suggests that the days of the Alawite supremacy will soon come to an end.

David Butter is a Middle East analyst