High-throughput experimental technology has provided insight into the inner functioning of plants. The current experimental technology facilitates the study of plant systems in a holistic manner, measuring observables from the genome, proteome, and metabolome up to the level of the ecosystem. The call for a systemic view in plant research is being made from multiple research fields. Although not yet fully developed for tree research, data sources are also rapidly growing in this area. Nevertheless, there are challenges and pitfalls in dealing with such increases in data. Some of these difficulties are deeply rooted in the complexity of the evolutionary systems. The lessons from complexity theory are rooted in studies performed several decades ago. Honouring principles that were formulated before bioinformatics and systems biology had been introduced facilitates the derivation of analytical methods with the potential to overcome these challenges in several ways.