Analyzing Heterogeneous Complexity in Complementary and Alternative Medicine Research: A Systems Biology Solution via Parsimony Phylogenetics

Abstract

Systems biology offers cutting-edge tools for the study of complementary and alternative medicine (CAM). The advent of ‘omics’ techniques and the resulting avalanche of scientific data have introduced an unprecedented level of complexity and heterogeneous data to biomedical research, leading to the development of novel research approaches. Statistical averaging has its limitations and is unsuitable for the analysis of heterogeneity, as it masks diversity by homogenizing otherwise heterogeneous populations. Unfortunately, most researchers are unaware of alternative methods of analysis capable of accounting for individual variability. This paper describes a systems biology solution to data complexity through the application of parsimony phylogenetic analysis. Maximum parsimony (MP) provides a data-based modeling paradigm that will permit a priori stratification of the study cohort(s), better assessment of early diagnosis, prognosis, and treatment efficacy within each stratum, and a method that could be used to explore, identify and describe complex human patterning.

An Integrative CGH, MSI and Candidate Genes Methylation Analysis of Colorectal Tumors

“…Briefly, to find out the distribution of aberrations for each specimen in relation to the total aberrations of all specimens the following procedure was carried out: all aberrations of all the cancer specimens were summed up and the duplicates removed; each specimen's aberrations list was compared to the total list of aberrations and each aberration scored as present (1) or absent (0), this polarity assessment produced a new data matrix of CGH data. The new data matrix was processed for maximum parsimony with MIX algorithm (of the PHYLIP analytical package to produce the cladograms [26] , [35] .…”

Potential self-regulatory mechanisms of yoga for psychological health

“…For example, studies that employ non-linear dynamical models of self-organization and emergence may capture not only the integration of top-down and bottom-up neurological processes involved in the proposed self-regulatory mechanisms of yoga, but also the dynamic relationships of these processes to psychosocial and clinical outcomes ( Pincus, 2012 ). Study designs that incorporate measures of heterogeneity, such as parsimony phylogenetics to define randomization groups and pattern or network analysis instead of analysis of averages, may respectively result in stronger comparison groups and more accurate representation of results than traditional randomized controlled trial designs ( Abu-Asab et al, 2012 ). For example, in a study of tai chi in older adults with peripheral neuropathy, a complexity measure of postural control based on multiscale entropy analysis was able to detect significant changes that were correlated with improvements in function as opposed to linear analyses of traditional outcomes which failed to detect these changes ( Manor et al, 2013 ).…”

Whole Complementary and Alternative Medical Systems and Complexity: Creating Collaborative Relationships

“…We organized participant workgroups and chose the papers for this issue to address the complexity of living systemsacrossdifferentlevelsoforganizationalscaleinWS-CAM research, i.e., biology, intra-individual and interpersonalpsychology,andlargersocialorganizations.Inaddition to introducing how complexity science can describe system behaviorsduringthepatient'sprocessofchangeandhealing duringtreatment [29,31,32],otherpapershereintroducethe readertoseveralofthebest,mostaccessiblemethodological exemplarsapplicabletoWS-CAMresearch.Thus,parsimoniousphylogeneticanalysis(biology) [33],statespacegridanalysis (psychology and social psychology) [34], and network analysis (organizations and societies) [35] demonstrate how scientists can apply complex systems thinking to investigate clinical and social phenomena that exhibit emergent properties and elude mechanistic reduction to singular causal relationships. To date, additional outcomes of the interexaminebiopsychosocialperson-centeredoutcomes.During this5thbiennialmeetingheldinSt.Croix,MN,awiderrange ofparticipantswasinvitedtotakepart.…”