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It was with a certain chilling confidence that the commander of an Islamist brigade explained his vision of Syria's future:

"The problem right now," he said, "is that the West refuses to help us. They refuse to help us because they don't want to help 'terrorists'. But we are not the terrorists. We are the ones winning this revolution. We are the ones helping the Syrian people. If the West helps us topple the regime, we will work with them. But if they invade Syria after the regime has fallen, to support the thieves and infidels in the secular opposition, then we will know that their real war is against Islam."

The commander – a Dutch dentist of Syrian origin who called himself simply 'Doctor' – was a member of the Ahrar al-Sham, the most powerful Islamist group in the vast array of factions fighting against the Syrian regime. His was a common perspective amongst the Salafi Islamists I met in northern Syria: measured, well-thought out and intellectually consistent, drawing on the realities of a war inexorably descending into factional chaos. Syria is on a knife's edge, they told me. The regime will fall but most didn't expect the fighting to end there. They feared a larger sectarian war and were practically begging the international community to help them prevent it.

It was a stark contrast to the few jihadists I encountered, whose only cerebral quality seemed to be their proficiency with weapons. Those men, aligned with the al Qaeda-linked Jabhat al -Nusra, spoke in terms familiar to a Western audience: global jihad, the re-establishment of the Caliphate, and, most frighteningly, perpetual war until their rule over Muslims is achieved.

Conflating the two groups is like mixing Christian fundamentalists with the Amish. And yet, Western governments continually cringe at the thought of Islamists, particularly Salafis, gaining a foothold in the various revolutions playing out in the so-called Arab Spring.

Among those, Syria is without a doubt the most complicated. But in many ways, it shares basic commonalities with the others: economic deprivation and large majorities of educated youth desperate for a better future. These factors sparked the uprisings – in Tunisia, Egypt, and Libya – and led to the collapse of self-interested oligarchs.

But what came next is arguably more important: Islamists dominated the newly-instituted democratic processes. From an-Nahda in Tunisia to the Muslim Brotherhood in Egypt, Islamists have swept elections by demonstrating a deeper understanding of the problems facing their people than the secularists.

Syria is no different. The Ahrar al-Sham has proven itself to be honest and genuinely concerned with the welfare of Syrians. The internally displaced laud their efforts: distributing aid in camps throughout the country, even risking themselves at the front lines to make sure people have food and water. They are winning hearts and minds, which will play in their favour when the time comes to form a new government in Syria.

The jihadists are lagging far behind on that front. Obsessed with jihad, they pay little attention to the suffering of civilians. The commander of one jihadist group, the Shohada al-Badr, put it to me this way: "If we get aid supplies, we will distribute it to our fighters first. They are the ones fighting the jihad so they need it. Then, if there is anything left over, we will give it to the people."

The difference between Salafis and al-Qaeda-style jihadists is nothing new for anyone who has followed the rise of orthodox Islam over the past few decades. Four Lions, the critically acclaimed British comedy following the antics of a group of homegrown British jihadists, pointed out what should be obvious to Western governments: the two groups don't even like each other that much. But in the film, the bumbling band of jihadists fails to catch the attention of British authorities while pious, non-violent Salafis are rounded up and renditioned to Egypt.

In the darkness of that comedic twist, the makers of Four Lions get it right. The West's allergy to orthodox Islam undermines its awareness of the real danger – jihadists who fail to understand even the most basic tenets of their religion and rather than educating Muslims (including themselves) instead want to forcefully impose their rather superficial ideology on them, by force if necessary.

Western governments, in Europe in particular, have shown a startling lack of understanding of those fundamental differences, something I wrote about in a commentary last year. They have failed to recognize the forces at play in Muslim communities both domestically and across the Middle East. Salafis are successful at this historical moment because Islam is in crisis and Muslims are seeking out guidance. The Salafi approach – literal and obsessed with ritual at the expense of a more holistic and spiritual understanding of Islamic principles – is simple and straightforward. Its simplicity is its strength and what attracts adherents.

This is also its weakness and what will ultimately prove its downfall as a political movement. The complexities of governing in the 21st century will expose Salafism to the harsh realities of political life. Salafis who enter the political arena will either have to change – to moderate – or fade away.

This is what western governments have failed to grasp. In Syria, the West has stood back and watched as the regime devastates its civilian population, fearing that helping the opposition is tantamount to helping Islamists. But in not helping, in desperately seeking to support secularists, they are setting the stage for a future conflict that will only strengthen the narrative of the jihadists. It will be a war of East versus West, the fulfillment of Samuel Huntington's Clash of Civilizations thesis.

That paper-thin theory predicting an amorphous Western culture in perpetual conflict with an equally vague Islamic world is not an inevitability. And yet, Western governments seem to be doing everything to make sure that clash happens.

Adnan Khan is a writer and photographer who lives in Istanbul and Islamabad.