response to the editors peter w. hochachka., thomas p. mommsen and patrick j. walsh

2
Ž . Comparative Biochemistry and Physiology Part A 130 2001 205206 Response to the Editors Peter W. Hochachka, Thomas P. Mommsen and Patrick J. Walsh At the outset, let us thank the editors of this journal for the compliment of reprinting the orig- inal article on EcoGenomics and the opportunity to broaden the scope beyond the realm of im- munology. They have clearly understood the in- tent of EcoGenomics and added some depth of their own. In this response, the senior author has been joined by a colleague that was instrumental in developing the perspective of EcoGenomics. We seek to make a couple of points that may not have been clearly elucidated and to solicit some support for an alternative view of priorities for genomic sequencing projects. EcoGenomics comprises three tiers of organi- . zation: 1 the assembly of molecular components . into a living organism, 2 the interaction and response of these components with the environ- . ment and 3 the dynamic interplay between species in ecosystems and impact of the environ- ment on that dynamic. The editors have added yet a fourth component of evolutionary history and phylogeny to this construct. Along the way the editors have introduced yet another term to the vocabulary, ‘functional phenomics’. If we un- derstand it correctly, phenomics is to the pheno- type what genomics is to the genotype. When we add all the other -omics, what we come away with is just Biology. In other words, the subject matter has not changed, it is our perspective and ability to deal with the complexity of life that has changed. We are struggling to find the words to describe the new insights and this struggle de- monstrates the vitality of the profession. These insights may well form the basis of an integrative revolution in biology, a consilience, which has not been seen since the Modern Synthesis. The addition of phylogenetic history to EcoGenomics, is a subject with which we have been struggling and is not yet clear to us. More than a quarter of a century ago, Prager and Ž . Wilson 1975 voiced the opinion that the mor- phological diversity might stem more from gene expression differences than from nucleotide dif- ferences per se. In the present context, the phylo- genetic information is not the basic instructions, but rather, in the amplification of information from genome to phenome. The extensive phenomic information documented by the expres- sion array data apparently fulfills the original Ž requirement of Numerical Taxonomy Sneath and . Sokal, 1973 that if enough traits are measured the discrimination between groups becomes inde- pendent of the choice of traits. Cladistic analysis is clearly different in form and philosophy as it emphasizes synapomorphic characters. As these characters accumulate on branches of a tree, the resulting topology is considered to be increasing supported. However, neither methodology con- siders the persistent and extensive interdepen- dencies between individual traits. Consequently, a few structural changes may be reflected in exten- sive functional pattern alteration and, on the con- trary, extensive structural changes may be absorb- ed by a resilient functional pattern. The proposed EcoGenomic approach measures phenomic rela- tionships by the information required to describe the differences in expression. This solution has the important effect that correlated phenomena will be counted only once, thus better accessing changes at the structural level. It is not clear if this approach will lead to the correct tracing of phylogenetic trajectories from phenomic informa- tion. However, by replacing the number of pheno- typic traits by the degrees of freedom contained in the phenomic information, the resulting 1095-643301$ - see front matter 2001 Elsevier Science B.V. All rights reserved. Ž . PII: S 1 0 9 5 - 6 4 3 3 01 00418-4

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Page 1: Response to the Editors Peter W. Hochachka., Thomas P. Mommsen and Patrick J. Walsh

Ž .Comparative Biochemistry and Physiology Part A 130 2001 205�206

Response to the Editors Peter W. Hochachka, ThomasP. Mommsen and Patrick J. Walsh

At the outset, let us thank the editors of thisjournal for the compliment of reprinting the orig-inal article on EcoGenomics and the opportunityto broaden the scope beyond the realm of im-munology. They have clearly understood the in-tent of EcoGenomics and added some depth oftheir own. In this response, the senior author hasbeen joined by a colleague that was instrumentalin developing the perspective of EcoGenomics.We seek to make a couple of points that may nothave been clearly elucidated and to solicit somesupport for an alternative view of priorities forgenomic sequencing projects.

EcoGenomics comprises three tiers of organi-.zation: 1 the assembly of molecular components

.into a living organism, 2 the interaction andresponse of these components with the environ-

.ment and 3 the dynamic interplay betweenspecies in ecosystems and impact of the environ-ment on that dynamic. The editors have addedyet a fourth component of evolutionary historyand phylogeny to this construct. Along the waythe editors have introduced yet another term tothe vocabulary, ‘functional phenomics’. If we un-derstand it correctly, phenomics is to the pheno-type what genomics is to the genotype. When weadd all the other -omics, what we come away withis just Biology. In other words, the subject matterhas not changed, it is our perspective and abilityto deal with the complexity of life that haschanged. We are struggling to find the words todescribe the new insights and this struggle de-monstrates the vitality of the profession. Theseinsights may well form the basis of an integrativerevolution in biology, a consilience, which has notbeen seen since the Modern Synthesis.

The addition of phylogenetic history toEcoGenomics, is a subject with which we have

been struggling and is not yet clear to us. Morethan a quarter of a century ago, Prager and

Ž .Wilson 1975 voiced the opinion that the mor-phological diversity might stem more from geneexpression differences than from nucleotide dif-ferences per se. In the present context, the phylo-genetic information is not the basic instructions,but rather, in the amplification of informationfrom genome to phenome. The extensivephenomic information documented by the expres-sion array data apparently fulfills the original

Žrequirement of Numerical Taxonomy Sneath and.Sokal, 1973 that if enough traits are measured

the discrimination between groups becomes inde-pendent of the choice of traits. Cladistic analysisis clearly different in form and philosophy as itemphasizes synapomorphic characters. As thesecharacters accumulate on branches of a tree, theresulting topology is considered to be increasingsupported. However, neither methodology con-siders the persistent and extensive interdepen-dencies between individual traits. Consequently, afew structural changes may be reflected in exten-sive functional pattern alteration and, on the con-trary, extensive structural changes may be absorb-ed by a resilient functional pattern. The proposedEcoGenomic approach measures phenomic rela-tionships by the information required to describethe differences in expression. This solution hasthe important effect that correlated phenomenawill be counted only once, thus better accessingchanges at the structural level. It is not clear ifthis approach will lead to the correct tracing ofphylogenetic trajectories from phenomic informa-tion. However, by replacing the number of pheno-typic traits by the degrees of freedom containedin the phenomic information, the resulting

1095-6433�01�$ - see front matter � 2001 Elsevier Science B.V. All rights reserved.Ž .PII: S 1 0 9 5 - 6 4 3 3 0 1 0 0 4 1 8 - 4

Page 2: Response to the Editors Peter W. Hochachka., Thomas P. Mommsen and Patrick J. Walsh

Response to Editors206

phenomic relationships are bound to be betterestimators of phylogenetic relationships becausethey better use function as means to access struc-tural change. We have no doubt that this opinionwill cause intense debate in phylogenetic circles.

Since the original article on EcoGenomics wasŽ .written, O’Brien et al. 2001 have listed a series

of criteria for selecting mammalian species forsequencing. In that article, the viewpoint appearsto be that mammals are a particularly significantgroup because they gave rise to us. Selectingorganisms for sequencing because they share tax-onomic affinities with humans is a rather narrowview of the living world. It isn’t that we should puttaxonomy aside as comparisons of related speciescan add considerable depth to our understandingof life. However, we should also ask what ecosys-tems need the attention of the enormous capacitygenerated by the Human Genome Project? Arehuman ancestors, diseases, agricultural speciesand model organisms the limit of our vision or isit time to redirect some of the resources to un-derstanding the biological systems that supportthis planet? Once this is decided, the selection ofspecies will be much easier. The Marine Genomicsprogram initiated in Charleston, SC chose to fo-cus on aquatic ecosystems and has targeted shrimpŽ . Ž .Gross et al., 2001 , oysters Jenny et al., in press ,stingrays, fish, and corals among others for ESTsequencing projects. It is clear that others shareour belief that non-model organisms hold a wealthof information concerning biochemical and physi-

Žological responses to environmental change cf..Gracey et al., 2001 . The value of this information

to basic science is unquestionable, but its signifi-cance to our stewardship of this blue orb cannotbe overestimated.

The emphasis on the integration of ecologicalsystems and metabolic processes embodied inEcoGenomics is ideally suited to the goals of thisjournal. It is the comparative aspects of genomesmanifested though their biochemical and physio-logical processes that give context and meaning tothe results. The interaction of these processeswith the environment, and what we do with thatinformation, gives the research a purpose. Theeditors of this journal have understood the intent

of EcoGenomics exactly and it is intoxicatingstuff.

R.W. ChapmanMarine Resources Research Institute,

South Carolina Department of Natural Resources,and Marine Biomedicine and En�ironmental

Science Program,The Medical Uni�ersity of South Carolina,

Charleston, South Carolina 29412,USA

Jonas AlmeidaDepartment of Biometry and Marine

Biomedicine and En�ironmentalScience Program,

The Medical Uni�ersity of South Carolina,Charleston, South Carolina 29412,

USA

References

Gracey, A.Y., Troll, J.V., Somero, G.N., 2001.Hypoxia-induced gene expression profiling in theeuryoxic fish Gillichthys mirabilis. Proc. Natl. Acad.Sci. USA 98, 1993�1998.

Gross, P.S., Bartlett, T.C., Browdy., C.L., Chapman,R.W., Warr, G.W., 2001. Immune gene discovery byexpressed sequence tag analysis of hemocytes andhepatopancreas in the Pacific White Shrimp, Litope-naeus �annamei, and the Atlantic White Shrimp, L.

Ž .setiferus. Dev. Comp. Immunol. 25 7 , 565�577.Jenny, M.J., Ringwood, A.H., Lacy, E.R., Lewitus, A.J.,

Kempton, J.W., Gross, P.S., Warr, G.W., Chapman,Ž .R.W. in press . Potential indicators of stress esponse

identified by expressed sequence tag analysis ofhemocytes and embryos from the American Oyster,Crassostrea �irginica. Marine Biotechnology.

O’Brien, S.J., Eizirik, E., Murphy, W.J., 2001. Onchoosing mammalian genomes for sequencing. Sci-ence 292, 2264�2266.

Prager, E.M., Wilson, A.C., 1975. Slow evolutionaryloss of the potential for interspecific hybridization inbirds: a manifestation of slow regulatory evolution.Proc. Natl. Acad. Sci. USA 72, 200�203.

Sneath, P.H.A., Sokal, R.R., 1973. Numerical Tax-onomy. W.H. Freedman & Co., San Francisco, 573pp.