IN the past few weeks there has been little to suggest that President Karzai, let alone the Afghan people, continue to think of Pakistan and Afghanistan as “conjoined twins”, a phrase that President Hamid Karzai had coined some years ago.

What we saw, instead, in the Afghan media and in the statements of Afghan parliamentarians, was condemnation of “unprovoked” Pakistani shelling of Afghan villages in Kunar province, from where the Tehrik-i-Taliban Pakistan’s Mullah Fazlullah and his men had been launching attacks against Pakistan, and a violent rejection of the proposed Strategic Partnership Agreement. (The latter, according to our reports, had been proposed by President Karzai himself to President Asif Ali Zardari in New York.)

We also saw the setting of impossible conditions for such an agreement by President Karzai and, last but not least, heard complaints that the Afghan Transit Trade Agreement was not being implemented by Pakistan causing grievous losses to Afghan traders.

In this very polluted atmosphere it was heartening to note the reaction in Afghanistan to the Taliban attack on Malala Yousufzai, now being treated in a hospital in Birmingham, and her two school friends. Not only did President Karzai telephone President Zardari to convey his condemnation of the attack and his sympathy for the family but in a very touching gesture the Afghan education ministry organised a prayer for Malala last Saturday in 16,000 schools across the country.

Some Afghan commentators pointed out that this gesture of solidarity came despite the fact that no such solidarity or sympathy had been expressed by Pakistan when hundreds of Afghan girls’ schools were faced with poison attacks by the Taliban and dozens of girls’ schools were burnt down or closed because of the intimidation by the Taliban. While this was not the main theme of the Afghan media, it does tend to highlight that despite viewing Afghanistan as a “conjoined twin” our media and our policymakers have been too pusillanimous to condemn inhuman actions by the Taliban in Afghanistan.

The Afghan gesture was prompted, perhaps, by a humanitarian impulse but there is no doubt that the Afghan government was seeking also to convey the message that both Pakistan and Afghanistan face the same existential threat from the same obscurantist forces.

There is no doubt either that they hope the public outrage in Pakistan, stronger perhaps than was provoked by the video showing the flogging of a Swati girl by Taliban persecutors, will mean the authorities will take the action that was implicitly if not explicitly promised in Gen Kayani’s statement when he was at Malala’s bedside and subsequently at what was said during the meeting of the joint chiefs of staff.

The world may hold over-centralised and incompetent governance, corruption, nepotism, warlords and the endemic distrust between the governors and the governed, along with resentment of the foreign presence, responsible for the resurgence of the Afghan Taliban. But from the Afghan government’s perspective the only problem is the safe havens the ‘armed opposition’ has in Pakistan. The Afghan claim is exaggerated but the fillip that our own Taliban receive from the presence of the Afghan Taliban cannot and should not be underestimated.

The sectarian killings, particularly of Hazaras in Balochistan, are by my reckoning laid at the door of our own extremist organisations but there is a well-known animus of the obscurantist Afghan Taliban towards the Hazaras and it would be reasonable to suspect that they have provided at the very least some support for these killings.

The most benign interpretation of our tolerance of the Afghan Taliban presence on our soil has been that they have a part to play in any future Afghan dispensation. But the time for negotiating what that role should be is now running out. Unfortunately, reconciliation seems to be something that is talked about but on which no progress is being made.

In a powerful and much longer than usual editorial recently, the New York Times has made the case that America must complete its pullout by end 2013 and not 2014 as currently planned. The point this editorial makes is that $500bn spent, 2,000 American soldiers dead, 45 per cent of returning Americans claiming disability benefits are all part of a price that is too high to pay when “the last chance of achieving victory evaporated when American troops went off to fight a pointless war in Iraq”.

The editorial has obviously been some time in the making. It reflects the general public view in America that the US must withdraw from any military commitment in Afghanistan. More importantly, withdrawal by end 2013 rather than 2014 is also a view that I have heard expressed by retired but extremely experienced, influential and hard-headed members of the American security establishment.

It is a view that has gained further credence following the exponential increase in ‘green on blue attacks’ and the conspicuous absence of any action on Karzai’s part to live up to the commitments made at Tokyo on curbing corruption. Instead, most American observers see his recent reshuffle of ministers and governors as steps taken to ensure that even if he does step down in 2014 as he has promised, he will be able to dictate the course of the election. The NYT editorial argues, in this context, that if the final mission for 2014 is to provide security for the 2014 elections this “seems dubious at best” and will only “lend American approval to a thoroughly corrupt system”.

Currently, Eklil Hakimi, the Afghan ambassador in Washington, and Ambassador James Warlick, Marc Grossman’s deputy, are in Kabul to commence negotiations on the terms and conditions for a residual US troop presence after the completion of Nato withdrawal in 2014. Afghan national security Adviser Rangin Dadfar Spanta is speaking about Afghan reluctance to grant immunity from local jurisdiction to such American troops.

To my mind this is now academic. The prospect for a continued American presence after 2014, if they do stay that long, is dim. Assistance promised at Chicago for the armed forces and at Tokyo for economic assistance may be forthcoming if Afghanistan establishes greater accountability but even that is doubtful. Afghanistan, one can foresee, will be in serious trouble economically and politically.

I have been arguing in these columns for the last few months that Pakistan must recognise that this is the direction in which the endgame in Afghanistan is headed. The Malala incident is a warning that unless civil society and our military and political establishment pull together and start a cleaning operation Pakistan will go in the same direction and will not be in any position to cope with the fallout from the brewing Afghan crisis.

The writer is a former foreign secretary.