Mr Lynn said there was nothing in the Habitats Directive which says there should be criminal sanctions. A criminal offence was introduced by the minister but the most the directive could have given rise to was penalties and not criminal liabilities, he submitted.
Counsel for the State, Conor Power SC, said Mr Lynn was attempting to overturn a Supreme Court decision related to milk quotas known as Maher v the Minister for Agriculture (2001).
Mr Power said the Habitats Directive imposed a positive obligation on the State that a series of measures must be taken to conserve. How else could the Directive be effectively transposed into Irish law, he asked.
The case was answered by the State's obligations to take all appropriate steps to prevent deterioration in listed sites, of which Moanveanlagh Bog is one, Mr Power said.
Reserving judgment, Mr Justice Garrett Sheehan, who sat with Mr Justice Alan Mahon and Mr Justice John Edwards, said the court would deliver its decision as soon as possible.
Independent TD Michael Fitzmaurice was present in the Court of Appeal for the hearing.
Dismissing the men's High Court case in August 2015, Ms Justice Iseult O'Malley said it seemed to her that the introduction of criminal sanctions, almost twenty years after the Habitats Directive came into being, can fairly be said to have been necessary for the proper implementation of that Directive.
The fact that it does not call for the creation of criminal offences was not, in Ms Justice O'Malley's view, decisive, since directives by their nature leave the choice of implementation methods to the member states.
She said no authority had been referred to which might suggest that criminal sanctions cannot be created unless the “parent” directive - in this case the Habitats Directive - calls for them.
The applicants do not themselves claim ownership of “turbary” rights, that is, the right to cut turf in Moanveanlagh Bog.
Mr O'Connor describes himself as an agricultural contractor, working on contract for farmers in his local area of Co. Kerry. Mr McCarthy is a machine operator employed by Mr O'Connor.
Both men assert that various families living on or near Moanveanlagh Bog have turbary rights and have taken turf from it for generations.
It is further asserted that these owners of turbary rights oppose the designation of the bog as a Special Area of Conservation and allege that their property rights have been infringed by the designation process.
The applicants aver that it is their understanding that the owners claim that they are entitled to continue to exercise their rights.
In the High Court, Francis Donohoe of the National Parks and Wildlife Service stated that between the late 1990s and 2002, arising out obligations imposed on Member States by the Habitats Directive, a total of 53 individual bog sites were nominated for designation as Special Areas of Conservation.
In 1999, the then Minister decided to prohibit commercial turf extraction on raised bogs which had been proposed for designation. She provided, however, for a 10-year period of “derogation” during which individuals could continue to cut turf subject to certain restrictions.
She also established a scheme for the purchase by the State of freehold ownership or turbary rights in affected areas.
In May, 2010 on foot of receipt of a report by an inter-Departmental working group in relation to the legal obligation to provide effective protection for raised bogs, the Government decided that turf cutting should cease immediately in the 31 sites that had been selected for designation between 1997 and 1999. It was also decided that cutting would cease at the end of 2011 for the sites selected in 2002.
Mr. James Ryan, a Wildlife Inspector in the Department who described himself as “the Irish national expert on raised bog conservation and restoration”, swore an affidavit on the effects of turf-cutting in raised bogs.
He stated that turf-cutting has both direct effects (by removal of habitat) and indirect effects (by drying out the bog system, thus affecting capacity to support the habitat). Almost all raised bogs in Ireland have been subjected to cutting, many for centuries, and many have been cutover or cutaway completely.
There are no completely intact raised bogs left in the country. Only 1,639 hectares of “intact” high bog can now be classified as Active raised bog and of the remainder, only 11% is considered to have significant potential for restoration, according to Mr Ryan.