We shed light on the disruptive advances brought by the ubiquity of computing and communication environments, which link devices and people in unprecedented ways into a new kind of techno–social systems and infrastructures recently named 'cyber-physical ecosystems' (CPE). While pointing to fundamental biases that prevent the traditional engineering school of thought from coping with the magnitude in scale and complexity of these new technological developments, we attempt to lay out the foundation for a new way of thinking about systems design, referred to as emergent engineering. One major characteristic of CPE is that, given their very nature, they cannot be a priori defined but rather emerge from the interactions among a myriad of elementary components. We show how this emergence can be guided by balancing positive and negative feedback, which tunes the growth of new configurations and adapts the system to sharp and unexpected changes. Rather than attempting to design the system as a whole, the components of the system are endowed with capabilities of dynamic self-assembly, disassembly and re-assembly to enable 'evolve-ability'. As paradoxical as it may seem to the classically trained systems engineer, this new attitude of the designer as an 'enabler' (vs. 'dictator' of a system's blueprint) allows the system to seamlessly adapt its development and evolve to meet dynamic goals and unexpected situations in an anticipative manner – an impossible feat under the traditional approach. To the extent that it produces new functionality, the proposed method enables a system to evolve via its ability of pervasive adaptation. Emergent engineering lies at a boundary where theoretical discovery meets systems engineering, computing and communications into a new convergent science of complex systems design. It currently transforms systems and software engineering by embracing various highly interdisciplinary perspectives.