As pointed out by the reviewers, these are the strengths and weaknesses of the paper: STRENGTHS The paper addresses the problem of converting a continuous-time Markov process model (MPM) to a structural causal model (SCM). The main advantage of such conversion is that it enables counterfactual inference in non-linear dynamic systems. This is demonstrated through two molecular biology case studies. FOR IMPROVEMENT The authors need to improve the presentation significantly, in order to make the paper accessible and readable. Another important point that should be addressed is the soundness and completeness of converting MPM to SCM.