  Examining individual components of cellular systems has been successful in
uncovering molecular reactions and interactions. However, the challenge lies in
integrating these components into a comprehensive system-scale map. This
difficulty arises due to factors such as missing links (unknown variables),
overlooked nonlinearities in high-dimensional parameter space, downplayed
natural noisiness and stochasticity, and a lack of focus on causal influence
and temporal dynamics. Composite static and phenomenological descriptions,
while appearing complicated, lack the essence of what makes the biological
systems truly "complex". The formalization of system-level problems is
therefore essential in constructing a meta-theory of biology. This work
examines key problems that cells must solve, serving as a template for such
formalization and as a step towards the axiomatization of biological
investigations.

Other Quantitative Biology;Biological Physics