GrandChallengesinComparative Physiology: Integration Across Disciplines and Across Levels of Biological Organization Donald L. Mykles,1,* Cameron K. Ghalambor,* Jonathon H. Stillman†,‡ and Lars Tomanekx *Department of Biology, Colorado State University, Fort Collins, CO 80523, USA; †Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA; ‡Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94703, USA; xCenter for Coastal Marine Sciences and Environmental Proteomics Laboratory, Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA Introduction the sixth paper in the ‘‘Grand understanding of the molecular mech- Challenges’’ series, which offers the anisms of cellular processes. The induc- Schwenk et al. (2009) provided an over­ view from comparative physiology. tive approach depends on observation view of five major challenges in organ- In this article, we expand upon three to develop universal principles. Charles ismal biology: (1) understanding the major challenges facing comparative Darwin, after all, used this approach to organism’s role in organism–environ­ physiology in the 21st century: vertical develop the theory of natural selection. ment linkages; (2) utilizing the func­ integration of physiological processes All too often these approaches are tional diversity of organisms; (3) across organizational levels within or- integrating living and physical systems viewed as mutually exclusive, when, in ganisms, horizontal integration of analysis; (4) understanding how fact, they are complementary and are genomes produce organisms; and (5) physiological processes across organ- used, to varying extents, by most biol­ understanding how organisms walk isms within ecosystems, and temporal ogists working today. Yet, we have the tightrope between stability and integration of physiological pro- fallen short of full integration across change. Subsequent ‘‘Grand cesses during evolutionary change. disciplines and levels of biological orga­ Challenges’’ papers have expanded on ‘‘Integration’’ is a key. It defines the nization. A major impediment for fur- these topics from different viewpoints, scope of the challenges and must be ther advancement has been the including ecomechanics (Denny and considered in any solution. Reductive limitations in tools and resources. Helmuth 2009), endocrinology and inductive approaches both have However, recent technological ad- (Denver et al. 2009), development of been used with great success in biology. vances (e.g., systems biology) give us additional model organisms (Satterlie The reductive approach employs a sim- an opportunity to combine reductive et al. 2009), and development of plified system to study a complex and inductive approaches to study theoretical and financial resources process. There is no question that emergent properties (Boogerd et al. (Halanych and Goertzen 2009). This is such an approach has yielded a greater 2007) and now allow us to entertain the notion that such a goal is possible, expression are just starting to be under­ develop extremely high-resolution and perhaps even achievable, within the stood and represent a potentially assays to compare transcriptome next decade. huge source of phenotypic variability (Gracey et al. 2008; Stillman and Organismal biology in general, and (Wu and Belasco 2008). Studies at Tagmount 2009), proteome (Dowd comparative physiology specifically, is each of these organizational levels re­ et al. 2010; Tomanek and Zuzow central to integration across disciplines. quire particular expertise and laborato­ 2010), and/or epigenome (Jablonka Others have promoted limited efforts ry resources, and these are often and Raz 2009) ‘‘fingerprints’’ of physi­ for vertical integration. ‘‘Macrophy­ customized for the organisms being ological ‘‘state.’’ These assays may siology’’ integrates ecology with physi­ studied. reveal very fine-scale differences ological ecology (Gaston et al. 2009). Krogh’s Principle (Krogh 1929; among individuals and/or populations ‘‘Functional genomics’’ integrates gene Krebs 1975), that ‘‘for such a large across ecologically relevant scales, but regulation with physiology (Dow 2007). number of problems there will be for elucidation of physiological mecha­ ‘‘Ecological genomics’’ applies molecu­ some animal of choice, or a few such nisms affected by those differences, lar techniques to the study of ecology animals, on which it can be most con­ these genomic–proteomic approaches (Ungerer et al. 2008; Pennisi 2009; Still- veniently studied’’ has been of central yield only hypotheses about which man and Tagmount 2009). We argue importance for organismal biologists genes may be involved in physiological that there is a need for integration and biomedical researchers alike processes. from genes to ecosystems across time (Satterlie et al. 2009). Organismal biol­ To directly test hypotheses resulting and space, in order to understand ogists use Krogh’s Principle to justify from ‘‘-omics’’ studies of nonmodel or­ and predict the effects of change in the study of a wide diversity of organ­ ganisms, we must turn to both classical the Earth’s climate, pollution, habitat isms that possess the appropriate com­ methods in protein biochemistry and change, invasive species, and over- bination of phenotype, ecology, and cellular physiology to determine what exploitation (Chown and Gaston 2008). evolutionary history for addressing spe­ specific gene products do, as well as Further, we discuss the three ‘‘inte­ cific questions of physiological adapta­ novel methods in reverse genetics gration’’ challenges in more detail and tion to a wide range of environmental (e.g., RNA interference) to determine then offer some guidance for the devel­ conditions. In contrast, biomedical bi­ what changes in phenotype occur opment of infrastructure, tools, train­ ologists use Krogh’s Principle to justify when those genes are not expressed ing, and shared resources that are a model organism-based approach, in (Dow 2007). Such studies require sub­ essential for addressing these chal­ which all fundamental questions about stantial resources to build necessary lenges. Included are initiatives to devel­ how organisms work can be addressed personnel and research infrastructure op model organisms that integrate in a relatively small subset of species specific to study organisms, as reverse vertically across all levels of biological that are readily cultured under labora­ genetic methods are often taxon- organization and address the social, po­ tory conditions, have a range of easily specific. Such infrastructure is already litical, and economic issues that are examined phenotypes, and, in some present for the small number of model fundamental to our ability to success­ cases, possess intrinsic high mutation organisms used by the biomedical re­ fully meet those challenges. rates that generate a wide range of phe­ search community, yet the challenges notypic variation. of translating a transcriptome profile Vertical integration of For a long while, organismal biolo­ into an integrated physiological re­ physiological processes gists studied a broad array of organisms sponse are still great. For example, across organizational but lacked the ability to develop mole­ Dow (2007) estimated that the cule–organism integration as the bio­ 300,000 researcher-years spent con­ levels within organisms medical research community has done ducting studies of the model arthropod Comparative physiologists study or­ for its relatively small set of study or­ Drosophila melanogaster have resulted ganisms at multiple levels of biological ganisms. Recent advances in high- in functional understanding of about organization, including the behavior throughput approaches to genomics 20% of the known genes, and those and metabolism of the whole organism, and proteomics have started to blur genes are, for the most part, associated isolated organs, the tissues of which what constitutes a model organism with developmental phenotypes for organs are made, cells that comprise (Crawford 2001; Gracey 2007; Dalziel which clearly indexed assays exist. As the tissues, cellular organelles (e.g., mi­ et al. 2009). Generation of genome se­ it is likely that many gene products tochondria), and components of organ­ quence for any study organism is now will function the same way across all elles, such as proteins and membranes. possible and will likely continue to organisms, we can reasonably predict In the past decade, cis-, trans-, and epi­ become both less expensive and more pathways and cellular roles of known genetic regulation of the genome, as in­ straightforward to do so in the future. genes for non-model organisms. dexed by changes in the transcriptome For organismal biologists interested in However, Dow (2007) suggests that a and proteome, have also become phe­ understanding physiological diversity third of the genes from any genome notypes of interest. Roles of regulatory across space and time (Gaston et al. are sufficiently novel that their func­ RNAs (e.g., endogenous miRNA and 2009), there is great promise for appli­ tion cannot be predicted without exogenous siRNA) in control of gene cation of genomics and proteomics to further empirical experimentation. Schwenk et al. (2009) suggested that an (e.g., genome, transcriptome, prote­ ability of organisms to build their cal­ important grand challenge to organis­ ome, and metabolome) and using cium-based shells, exoskeletons, and