Civil war within a civil war? Syrian rebel infighting raises new worries.

In Syria, Al Qaeda-linked rebel groups have been battling secular-leaning rebel groups near the Turkish border.

Syrian opposition fighters are seen at the top of a mountain in the vicinity of a rebel camp in Idlib province, Syria, Wednesday, Sept. 18, 2013.

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Here’s more evidence that the Syrian civil war may be mutating into something messier: Turkey shut a border crossing into Syria after an Al Qaeda-affiliated insurgent group clashed with fighters from the more secular-leaning Free Syrian Army.

That jihadi elements are actively fighting against Syrian President Bashar al-Assad’s forces is no secret to anyone paying attention. While the US and its allies—Western and Arab—have put their faith, funding, and to some degree, weaponry, in and to the FSA, many observers (not the least of which is Russia’s Vladimir Putin) have warned that the growing presence of jihadis from Iraq, Chechnya, Jordan and elsewhere  threatens to send the conflict careering into dangerous new territory. At least one such group, Jabhat al-Nusra, has been slapped with a “Foreign Terrorist Organization” designation by the US State Department.

The fighting this week between FSA units and the al-Qaida-allied Islamic State of Iraq and the Levant, is giving yet more credence to those fears, sending ripples of worry through policy makers’ minds from Ankara to Amman. According to many press reports, the Islamic State of Iraq and the Levant (ISIS - sometimes called the Islamic State of Iraq and Syria), on Thursday pushed other rebel groups out of the northern Syrian town of Azaz, close to the Turkish border. The town is a key conduit for people and supplies coming in and out of Syria.

There is no definitive estimate of the numbers of Al Qaeda linked fighters in Syria. New research from the British defense consultancy IHS Jane’s puts estimates of the number of al-Qaeda-linked fighters at about 10,000— or around one-tenth of the overall estimated number of insurgents fighting to topple Mr. Assad. 

The research was done by Jane’s analyst Charles Lister who a few weeks earlier predicted that internecine rebel warfare was inevitable.

The debate over Assad’s chemical weapons arsenal and who was responsible for using sarin gas in an attack last month has fixated the public for weeks now, momentarily eclipsing the discussion over what some are calling called Syrian blowback

The UN Security Council this week will continue to haggle over a resolution to take control of and destroy Assad’s chemical weapons. The devil is very much in the details, but if the seizure and destruction ever happens, it will be a small bright spot amid a violent and chaotic situation.

Will rebel infighting give Assad’s forces the upper hand in their effort to crush the insurgency? Do this week’s successes by Al Qaeda-linked groups along the Turkish border foreshadow similar efforts to come, as Mr. Lister predicts?

No one knows, but one thing’s sure: the Syrian war is likely going to get worse before it gets better.

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