Hierarchy and Information in a System Approach to Plant Biology: Explaining the Irreducibility in Plant Ecophysiology

The Challenge to Translate OMICS Data to Whole Plant Physiology: The Context Matters

“…Actually, the cell is the result of the properties that emerge from the complex interactions and spatial structures among the thousands of molecules and enzymes of which it is composed. In addition, the environmental context, whether from outside or inside the plant, contributes to shape the way that information is processed by each cell (Gilroy and Trewavas, 2001 ), and these properties expand at different scales within the plant (Souza et al, 2016 ). According to Vítolo et al ( 2012 ), the observation of different scales of plant organization, under the same circumstances, can show remarkable differences in the responses to the same stimuli, allowing different interpretations if considering each scale as isolated (Stressed or not stressed?…”

“…However, different constrains can make both the predictability and the controllability difficult from the bottom-up cause-effect approach that underpins the deterministic view of science based on an upward chain of causality (Figure 1 ) (Noble, 2008 ; Sheth and Thaker, 2014 ). The first “bottleneck” is how to integrate the massive datasets from molecular high-throughput technologies with the growing high-throughput information on the crop scale, i.e., plant phenomics (Fukushima et al, 2009 ; Tardieu et al, 2017 ), which is a typical problem of finding a proper (if it does exists indeed) scaling law (Souza et al, 2016 ).…”

“…The first “bottleneck” refers to the problem of emergent properties at the higher level organizations of the system that are not fully determined by the properties of the lower levels (Souza et al, 2016 ), for example, changes in the transcriptome or in the proteome do not always result in respective alterations in the metabolome (biochemical phenotype) that exhibits its own dynamics (Ryan and Robards, 2006 ). Additionally, there is the influence of downward causation processes (Noble, 2008 ) (Figure 1 ), when higher levels of organization affect the functioning of the lower levels.…”

Automatic classification of plant electrophysiological responses to environmental stimuli using machine learning and interval arithmetic

“…Plants as sessile and modular organisms face the challenge to keep their stability growing in environments under constant changing (Souza et al, 2016). Since plants lack a central command to organize the environmental information gathered in each module (e.g., a branch root or a leaf), an efficient communication system has evolved in order to integrate local information (cell-to-cell communication) and to signalize through the plant body (long-distance communication) (Trewavas, 2003;Lüttge, 2012).…”

Systemic research of plant growth and stress in a specially designed climatic hydroponics system

“…The functional and organizational properties of plants are now being investigated at different hierarchical levels, that is, from the ecosystem and plant population level to subcellular and molecular levels of studies (Souza, Bertolli, & Lüttge, 2016;Trewavas, 2006). Recent reviews have shown that the majority of studies have been conducted at the borders of this hierarchy range, that is, either at the molecular or at ecosystem level (Duran-Nebreda & Bassel, 2017).…”