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A company looking to become Carbon Neutral must first perform an audit to determine its emissions.  The Greenhouse Gas Protocol specifies Scope 1, 2, and 3 emissions from direct energy use (fuel burned on site), indirect energy use (energy purchased from utilities), and all other significant activities of the business, including raw materials purchased, transportation of goods, travel and commuting of employees, and leased assets such as office space.  

Such an audit would require getting data from every part of the business, from purchasing to manufacturing to facilities management to human resources.  This often involves manually gathering data and entering them into spreadsheets.  The data is then used to calculate emissions as part of lifecycle analysis, with software such as OpenLCA

In reality, much of this data may either be difficult to get or simply not available.  Sometimes data is simply not available, and generic model values from either free LCA repositories or proprietary ones have to be used.  At other times, the high cost or complexity of obtaining the data would require a judgement call about whether the activity is "significant" to the company's overall emissions or not.  

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