Tal­mu­dic Ques­tion #10

Yes, we do — if we all agree to say so. The or­gan­isms them­selves will, of course, con­tinue trad­ing and re­com­bin­ing snip­pets of ge­netic in­for­ma­tion ac­cord­ing to their own im­per­a­tives, with cal­lous dis­re­gard for our el­e­gant but clearly ar­ti­fi­cial cat­e­gories. Tax­on­o­mists will have to con­tinue puz­zling over prob­a­bly-un­re­solv­able is­sues like ex­actly how many top-level cat­e­gories there should be, or ex­actly when a va­ri­ety be­comes a species.
This hu­man ob­ses­sion with cat­e­go­riz­ing is ex­tremely use­ful for those of us who study life, which is why we need (and will al­ways need) those per­pet­u­ally frus­trated tax­on­o­mists. Their re­sults don't seem to have much to do with the re­al­ity at the cel­lu­lar level, though.

No, we don't- that's the beau­ti­ful thing about be­ing a sci­en­tist. There is so much that we don't know. Once we get com­fort­able in think­ing that we know some­thing, we get belted over the head with a new dis­cov­ery. Look at how many species of bac­te­ria are in the ocean that we cant cul­ture and we only know ex­ist be­cause of DNA fish­ing. Its ig­no­rant to be­lieve that we know every­thing. What we do know works for us now but the ex­cite­ment of what we don't know keeps us search­ing.

I won­der if fac­tit­ian has this right. In terms of the Sar­gasso sea project and other metage­nomics projects, here's a ques­tion; would we know it when we saw it? Af­ter all, the Ar­chaea as a third do­main wasn't ex­actly ob­vi­ous to all or eas­ily ac­cepted. We prob­a­bly have a de­cent idea of the phy­lo­ge­netic sig­na­ture (as­sum­ing we agree that rDNA se­quence or some other uni­ver­sal gene or gene set can be used), but the as­sump­tions are quite damn­ing, in terms of dis­cov­ery. Re­mem­ber (and I hope I have this right) that ex­tremophiles and methanogens were iden­ti­fied bio­chem­i­cally first, and only af­ter­wards rec­og­nized as a novel do­main. Peo­ple are re­mark­ably good at fit­ting even the odd­est things into a par­a­digm (as re­ferred by Alan in com­ment two). Fun to think about, as a tal­mu­dic ques­tion should be!