We lack robust frameworks for 'forward engineering' stochastic thermodynamic computation over molecular free-energy landscapes (which is basically what a "chemical soup" is doing) like we do for analog/optical/digital computing. This is why, as a field, medicine is so heavily empirical and reverse engineering oriented.
Man... I had to chatgpt your comment just to understand. But I do now.
Basically, unlike current chip manufacturing process where every stage is deterministic and precise, the soup-world, the chemistry, is not. And we do not have accurate enough models to handle them in deterministic way, or, model them precisely.
My respect for nature's engineering just shot up by 10 times more.