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For example, if one tries to look up research opportunities or browse papers in the field chemical biology, most often return research fields related to biological sensing, drug activity etc. and which the ultimate goal of all these researches are related to treating diseases of some kind.

http://pubs.acs.org/journal/acbcct

and only occasionally, do the other non disease treatment related sector of chemical biology (those related to proteins, environmental biochemistry, microbial reactors etc.) can be found

http://www.ch.cam.ac.uk/rig/biological/about

http://chemistry.mit.edu/research/biological

http://www.kemi.uu.se/research/molecular-biomimetic/microbial-chemistry/

Why are most chemical biology research dominated by disease treatment goals despite the chemistry of biological systems are not limited to the medical sector, or is it because the non disease related sector of chemical biology are often lumped into the environmental science, biotechnology and engineering sectors?

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Because when we try to sell some new molecule to the chemical biology journals' editors and reviewers we think health and drug like actions sell better than a mere signalling molecule or so ?