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The Ontario Court of Appeal has left little doubt that a key section of the Anti-terrorism Act should not have been struck down under the Charter of Rights in 2008.

Two of three judges hearing an appeal from convicted terrorist Momin Khawaja said Tuesday that the provision logically requires the Crown to prove a terrorist act was committed for political, religious or ideological reasons.

"Does the fact that police investigate whether you have a motive to kill someone make it unconstitutional?" Mr. Justice David Doherty asked defence counsel Lawrence Greenspon. "This is stunning to me."

Mr. Greenspon agreed that motive is "at the heart" of the act, but he argued that once the provision had been struck down, Mr. Khawaja tailored his defence to meet a case where motives were no longer relevant.

Should the court opt to reinstate the motive clause, Mr. Greenspon said, Mr. Khawaja must be granted a new trial.

The "motive clause" came under heavy debate in Parliament when it was created in the wake of the Sept. 11, 2001, terrorist attacks.

At Mr. Khawaja's trial, Mr. Justice Douglas Rutherford of Ontario Superior Court struck down the provision on the basis that it could lead to racial profiling and might chill free expression within specific religious or racial groups.

Judge Doherty scoffed at that notion Tuesday. "It is like saying that the crime of treason will stifle people expressing dissent because [individuals would be charged]if they drop a bomb on Parliament," he said.

Judge Doherty compared investigating terrorism to homicide investigations that focus on black gangs in high-crime areas of Toronto. To do so is sensible, he said, not a deplorable instance of racial profiling.

If police investigators misuse the provision to hound innocent Muslims, he said that misconduct can be corrected. He said that striking down the entire clause because of this fear is "nonsensical."

Mr. Justice Michael Moldaver agreed that it is foolish to assume police will act in bad faith against innocent people. He also noted that if the motive clause is removed from the act, bikers and mobsters could be charged with committing terrorist acts.

Convicted of five offences, Mr. Khawaja became the first person in Canada to be found guilty of facilitating terrorist acts.

He was sentenced to 10 and a half years in prison - in addition to the five years he had already served - for building parts of a bomb, training as a terrorist and financing terrorism through an intermediary.

A computer technician for the Foreign Affairs department, he met a band of British al-Qaeda sympathizers on the Internet and travelled to Pakistan, where he received paramilitary training and learned how to fire rifles and rocket-propelled grenades.

In 2007, five of his colleagues were convicted in Britain of plotting to bomb nightclubs and shopping malls.

Madam Justice Eleanore Cronk and Judge Moldaver went after another defence argument Tuesday; a claim that Mr. Khawaja was merely trying to aid Afghan insurgents engaged in a legitimate war.

They said that the insurgency is not an armed conflict that meets international standards of warfare. "This is all pie in the sky," Judge Moldaver said.

Crown counsel Nicholas Devlin told the court the motive clause quite sensibly distinguished acts of terrorism as being violence motivated by political, religious or ideological feeling.

"Without this motive element, [terrorism]is just an ordinary crime," he said. "Terrorism is different and that's why it is punished differently."