The role of excessive CO₂ in the Earth ocean-atmosphere system as a significant factor in causing the end-Permian mass extinction has been a subject of widespread research. CO₂ injected into the atmosphere by successive eruptions from the Siberian Traps has been postulated as a major factor leading to the end-Permian mass extinction by facilitating global warming and reduced ocean circulation, leading to overturn and/or upwelling of deep anoxic, euxinic and CO₂ rich waters. Although heretofore the focus on the role of excessive CO₂ has concentrated on these “bottom up” effects, “top down” effects of increasing atmosphere CO₂ concentrations on ocean surface waters and biota have not previously been explored. Due to current increasing anthropogenic input of atmospheric CO₂, this is one mechanism for biotic crisis that is becoming well-understood. Passive diffusion of atmospheric CO₂ into ocean surface waters decreases pH and [CO₃^-2] and thereby decreases the CaCO₃ saturation state of seawater; these effects cause a physiological and biocalcification crisis for many marine invertebrates that secrete calcareous skeletons by dissolving them, decreasing their degree and rate of calcification, and making it difficult for some to buffer intracellular fluids. Latest Paleozoic/earliest Mesozoic increases in atmospheric CO₂ would have led to increased ocean CO₂ levels, decreased seawater CaCO₃ saturation state, and therefore a biotic crisis in shallow marine waters. While both “bottom up” and “top down” mechanisms may have contributed to the relatively short term biotic devastation of the end-Permian mass extinction, such a “top down” physiological and biocalcification crisis would have had long-term effects and readily would account for the protracted 5-6 million-year-long absence of colonial metazoan reefs and reef organisms, opportunistic behavior of many groups of organisms, and decrease in size of a variety of benthic marine organisms (“Lilliput effect”) during the Early Triassic.

Undersaturation of seawater with respect to CaCO₃ was also likely a contributing factor to the end-Triassic, early Toarcian, and perhaps the end-Guadalupian mass extinctions. These ancient biocalcification crises are analogs for the fate of Earth's marine biota if anthropogenic input of atmosphere/ocean CO₂ continues to rise.