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Dr Mac Armstrong said that the move could save up to 1,000 lives a year in Glasgow alone.
Around 1.2 million Scots smoke and it is estimated that the habit causes about 13,000 deaths a year as well as costing the National Health Service £200 million.
Ireland introduced a ban last week and the Scottish Executive has outlined an action plan aimed at reducing smoking levels, which are the highest in the UK. Ministers will hold a consultation on a potential ban later in the year.
Jack McConnell, Scotland’s First Minister, has recently appeared to soften his personal opposition to an outright ban on smoking in public places.
In January he said that he was personally opposed to any such ban because he believed that it would be difficult to police and would be impractical. Last week, however, he said that he would retain an open mind about the Executive’s consultation on steps to create a “smoke-free Scotland”.
Mr McConnell also said that he would be using a forthcoming trip to Ireland to see how the ban was operating there.
Dr Armstrong argued in his annual report that a total ban on smoking in public places was a “clear, obvious and logical next step”.
He said: “I very much welcome the start of some real debate on these issues. I’m assuming that the motion for debate will be that there should be a ban on smoking in public places in Scotland and I am speaking strongly in favour of that motion. Such a ban is an essential component of our evolving tobacco control strategy.”
Dr Armstrong said that a ban on smoking in public places would satisfy the wishes of the vast majority of people in Scotland.
“It protects those who cannot choose, not only obvious groups like employees but children and the unborn. It also sends a strong message to all that smoking is not normal in Scotland and that we are not willing to tolerate the damage that it causes,” he said.
Dr Armstrong denied that his support for a ban put him at odds with Mr McConnell. “I don’t think there’s anything between us on this,” he said. “I think a ban on smoking in public places is a clear, obvious and logical next step. I think there’s good reasons and strong evidence behind it.”
Maureen Moore, the chief executive of the anti-smoking charity ASH Scotland, said that she was delighted with Dr Armstrong’s comments.
“A ban on smoking in the workplace would save many lives and send out a strong message to young people, who would see it is not accepted among adults,” she said.
Jim Coleman, deputy leader of Glasgow City Council, called on the Executive to accelerate its consultation on smoking curbs. “My own view is that each local authority should be given discretionary powers to adopt a smoking ban,” he added.
Last month officials in Tayside said that they planned to press ahead with proposals for a ban in public places. NHS Tayside announced that it wanted to make Dundee a smoke-free zone by 2007. The ban would apply to all public places including pubs, clubs and restaurants, but it would not apply outdoors.
Yesterday a Glasgow City Council committee sought to have stricter smoking controls imposed on licensed premises applying for children’s certificates.
Dr John Garner, chairman, of the British medical association in Scotland, said: “The Scottish Executive must act on this evidence and bring forward legislation to create smoke-free public places in Scotland.”
Stewart Maxwell, a Scottish National Party MSP who has lodged a Bill at the Scottish Parliament aimed at banning smoking in places where food is served, also welcomed Dr Armstrong’s comments.
An Executive spokesman said: “We’re launching a consultation, hopefully in June, and then we want the public to tell us what they think. It would be unfair for the Executive to make any prejudicial comment.”
Elsewhere in his report Dr Armstrong said that there was still much to do to improve diet and that drug misuse continued to take a heavy toll on the nation’s youth, with 382 drug-related deaths in 2002. He also reported increases in sexually transmitted diseases such as HIV, chlamydia and herpes. Heart disease and stroke deaths had continued to fall over the past ten years.
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