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The biogenic carbonate hard parts of fossil bivalves, cephalopods and brachiopods are among the most widely exploited marine archives of Phanerozoic environmental and climate dynamics research. The advent of novel analytical tools has led many workers to explore non-traditional geochemical and petrographic proxies, and work performed in neighbouring disciplines sheds light on the complex biomineralization strategies applied by these organisms. These considerations form a strong motivation to review the potential and problems related to the compilation and interpretation of proxy data from bivalve, cephalopod and brachiopod hard parts from the viewpoint of the sedimentologist and palaeoceanographer. Specific focus is on the complex biomineralization pathways of a given dissolved ion or food particle from its aquatic environment via the digestion and biomineralization apparatus in molluscs and brachiopods and its incorporation into a biomineral. Given that molluscs and brachiopods do not secrete their hard parts from seawater but rather from their mantle and periostracum, this paper evaluates differences and similarities of seawater versus that of body fluids. Cephalopods, bivalves and brachiopods exert a strong biological control on biomineralization that, to some degree, may buffer their shell geochemistry against secular changes in seawater chemistry. Disordered (amorphous) calcium carbonate precursor phases, later transformed to crystalline biominerals, may be significant in carbonate archive research due to expected geochemical offset relative to the direct precipitation of stable phases. A reasonable level of understanding of the related mechanisms is thus crucial for those who use these skeletal hard parts as archives of the palaeo-environment. The impact of what is commonly referred to as 'biological factors' on the geochemistry of mollusc and brachiopod hard parts is explored for conventional isotope systems such as carbon, oxygen, strontium and traditionally used element to calcium ratios. In particular, the often used d STATE OF THE SCIENCE the architecture of mollusc and brachiopod hard parts and their ultra-structures must guide sampling strategies for geochemical analyses. Where feasible, a detailed understanding of the diagenetic pathways and the application of multi-proxy and multi-archive approaches should form the foundation of fossil carbonate archive research. The uncritical compilation of large data sets from various carbonate-shelled organisms collected at different locations is not encouraged.

For the Quaternary and Neogene, aragonitic biogenic and abiogenic carbonates are frequently exploited as archives of their environment. Conversely, pre‐Neogene aragonite is often diagenetically altered and calcite archives are studied instead. Nevertheless, the exact sequence of diagenetic processes and products is difficult to disclose from naturally altered material. Here, experiments were performed to understand biogenic aragonite alteration processes and products. Shell subsamples of the bivalve Arctica islandica were exposed to hydrothermal alteration. Thermal boundary conditions were set at 100°C, 175°C and 200°C. These comparably high temperatures were chosen to shorten experimental durations. Subsamples were exposed to different 18O‐depleted fluids for durations between two and twenty weeks. Alteration was documented using X‐ray diffraction, cathodoluminescence, fluorescence and scanning electron microscopy, as well as conventional and clumped isotope analyses. Experiments performed at 100°C show redistribution and darkening of organic matter, but lack evidence for diagenetic alteration, except in Δ47 which show the effects of annealing processes. At 175°C, valves undergo significant aragonite to calcite transformation and neomorphism. The δ18O signature supports transformation via dissolution and reprecipitation, but isotopic exchange is limited by fluid migration through the subsamples. Individual growth increments in these subsamples exhibit bright orange luminescence. At 200°C, valves are fully transformed to calcite and exhibit purple‐blue luminescence with orange bands. The δ18O and Δ47 signatures reveal exchange with the aqueous fluid, whereas δ13C remains unaltered in all experiments, indicating a carbonate‐buffered system. Clumped isotope temperatures in high‐temperature experiments show compositions in broad agreement with the measured temperature. Experimentally induced alteration patterns are comparable with individual features present in Pleistocene shells. This study represents a significant step towards sequential analysis of diagenetic features in biogenic aragonites and sheds light on reaction times and threshold limits. The limitations of a study restricted to a single test organism are acknowledged and call for refined follow‐up experiments.