Ruby, my thinking of cells, in regards to the modularity topic, was of them being the basic units of the larger whole. However, it is certainly feasible to look at cells as a larger whole, made up of cellular components, nucleus, organelles, membranes, etc. So in this sense I agree that the "modularity" can go both ways. So I stand corrected.
However, I don't think this has anything to do with your larger point--that of absolute truth. Scientists don't claim anything to be absolutely true. All truth (with only one or two exceptions) is provisional. Where scientists land in the metabolism vs replication vs it's-a-bad-question debate has nothing to do with absolutes.