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But the government said policies such as those protecting the Green Belt, sites of special scientific interest, national parks and other areas could not "be overridden by the presumption".
BBC: UK Politics
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The findings, based on data from 80 Sites of Special Scientific Interest (SSSIs), also warned that the impact of overgrazing by deer had a knock-on effect that undermined woodland ecologies.
BBC: Roe deer numbers 'changing woodland ecosystems'
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It said the planned roads, and the upgrading of a railway line, would have very damaging effects on a number of sites of special scientific interest (SSSIs), the highest category of conservation protection.
BBC: Hastings bypass plan 'flawed'
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The UK has generally chosen to underpin the designation of its Ramsar sites through prior notification of these areas as Sites of Special Scientific Interest (SSSIs) (or Areas of Special Scientific Interest (ASSIs) in Northern Ireland).
UNESCO: UK National Commission for UNESCO - UNESCO Conventions, Recommendations & Declarations in the UK
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The list is to be used to decide which sites of special scientific interest (SSSI) should have money spent on them to prevent over-abstraction by water-companies, which is the process of removing water for domestic or industrial use.
BBC: Campaigners claim beauty spots 'at risk'