According to Mann and Kump (2015),
Geologic proxies are characteristics of sedimentary rocks that we can use to infer ancient environmental conditions. Climate scientists study proxies because there are no thermometer records or samples of ancient air from the geologic past. Proxies may even include the pores on fossil leaves: when atmospheric CO2 levels are low, plants need more pores to bring in more CO2. Under the microscope, well-preserved fossils reveal the number of pores; comparing this pore density to that of living plants allows scientists to establish CO2 levels in the geologic past.
However, in order to use this comparison to make inferences about CO2 levels, it seems to me that this would require establishing that everything else is held equal. If this is not established, it seems to me that this would not allow one to use plant pores as proxies for past CO2 levels and thus climate change. Therefore, my question is, how do researchers attempt to hold all else equal when comparing the pore density of fossilized plants to living plants to establish a causal relation between past CO2 levels and plant pores density?
Mann, M. E. and L. R. Kump (2015). Dire Predictions: Understanding Climate Change 2nd Edition. DK Publishing.