There is concern that selling the products of taxonomic work as individual units can distort the scientific process. Would it lead to increased splitting of taxa? For example, if a taxonomist is uncertain about whether to split or lump a taxon, the financial incentive might swing the balance so that double the profit could be made from the same work! Other questions come to mind. What happens if a name is sold but the paper publishing it is never written (thus it is not available under the Code)? What if the name is synonymized after the deal is done? Would the country of origin of the taxon be able to claim ownership of the proceeds from the sale of naming rights? Would a biodiversity-rich country be justified in raising its rates for research permits in anticipation that profit might be made from this aspect of the results of taxonomic exploration? Will much larger grants and even more complicated memoranda of understanding, be needed to cover the financial interests that have crept in to taxonomy through this means? Will institutions auction off the work of their scientists to help fund taxonomic research, but thereby remove one of the rewards of what is often perceived as otherwise punishing work, the privilege of choosing a name? Could there even be a total loss for the taxonomist, whereby they lose the right to choose a name due to its sale, and then the funds get claimed by the home country for the organism as a share of commercial profit from bioexploration?
In addition, while the charitable aspects are laudable and in some cases very successful, in other cases of selling names it is not clear how much of the price paid actually returns to those who need it most. There are also concerns that while naming charismatic species can command high prices, the taxa, ecosystems and taxonomists who need the support the most will not be able to raise funds this way. This could lead to a dreary situation that they become doubly disadvantaged, if the administrations that oversee them might expect them to raise research funds through selling names, but there are no buyers for their non-celebrity uncharismatic taxa.
A further set of objections revolve around the recommendations that scientific names should have some connection with the organism such as a descriptive aspect, its place of origin, an honourific for someone in the field (not a purchaser after the fact). People buying names may not want to give a biologically or geographically predictable name to the taxon.
Monetizing biodiversity is indeed a challenge.
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