In the Company of Microbes. Moselio Schaechter

major problems for macroorganisms).

      From this extended ecological point of view, we are embedded in a network of microbial interactions. This view is also reinforced from a phylogenetic perspective. If eukaryotes are indeed an odd kind of archaeon (Koonin and Yutin 2014; Spang et al. 2015) and humans just a very tiny twig in the eukaryote tree (Adl et al. 2012), then microbial phylogenetic knowledge allows us to realize even more conclusively our dependently evolved and maintained nature.

      Microbiome research and how it draws our attention to the organisms within us should not blind us to broader microbial ecology and evolution. There is a great deal of non-human-focused microbiome research currently unraveling the major evolutionary and ecological ties we have to the microorganisms running the planet. This, I suggest, is where “human nature” studies are ultimately located, and where they could help make more sense of our own glorification of our gut microbiota.

       Maureen O’Malley is a Senior Research Fellow in the Department of Philosophy, University of Sydney, and author of the book Philosophy of Microbiology.

       References

      Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EA, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick RS, Schoch CL, Smirnov A, Spiegel FW. 2012. The revised classification of eukaryotes. J Eukaryot Microbiol 59:429–493.

      Brüssow H. 2015. Microbiota and the human nature: know thyself. Environ Microbiol 17:10–15.

      Bouchard F, Huneman P (ed). 2013. Vienna Series in Theoretical Biology, p 17-36. In From Groups to Individuals: Perspectives on Biological Associations and Emerging Individuality. MIT Press, Cambridge, MA.

      Hutter T, Gimbert C, Bouchard F, Lapointe FJ. 2015. Being human is a gut feeling. Microbiome 3:9 10.1186/s401.68-015-0076-7.

Koonin EV, Yutin N. 2014. The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb Perspect Biol 6:a016188 10.1101/cshperspect.a016188.

      Kronfeldner M, et al. 2014. Recent work on human nature: beyond traditional essences. Philos Compass 9:642–652.

      Pradeu T. 2014. Galatea of the microbes. Philosophers’. Magazine 67:89–95.

      Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179.

      West SA, Griffin AS, Gardner A. 2007. Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection. J Evol Biol 20:415–432.

      August 31, 2015

       bit.ly/1OFxBuh

      #6

      by Elio

      With the buzz created by the discovery of giant viruses, e.g., Mimivirus, the distinction between viruses and cells is said to get blurred. I maintain that this is not the case because the single most important distinction is that viruses lose their corporeal integrity, cells do not. What do you think? Are you a blurrer or a non-blurrer?

      January 18, 2007

       bit.ly/1Xgrzli

13

      Good Writing Beats Bad Writing, Most Any Day

      by Elio

      There isn’t any thought or idea that can’t be expressed in a fairly simple declarative sentence...

      – E.B. White, Fro-Joy

      Just when some people believe that the world is going to hell in a handbasket, here I am, ready to make a cheerful personal statement: “Scientific writing is improving!” Of course I base this on reading the microbiological literature, but assume that it’s generally true. What makes me say so? Well, more often than not, current research papers and reviews contain a fair share of simple declarative sentences. In my earlier days, typical statements were often in the passive form: “The effect of X on Y has been studied.” The first person form is now accepted, much to everyone’s relief. And titles of articles tend to be informative. Gone is Studies on the Metabolism of Escherichia coli: Part XIV. And, although I couldn’t swear to it, I believe that the language in graduate student papers has also improved. Nowadays, even humor is permissible. It has even permeated this blog, as exemplified by the wicked sense of humor of my co-blogger, Merry Youle, who has come up with titles such as The Bacterium That Doesn’t Know How to Tie Its Own Shoelaces, Coxiella Escapes from Cell, and A Holin One.

What has happened? Have scientists turned into Thurbers overnight? Good question. I would guess that changes in culture (sensu lato) are the big factor. We seem to be more factual in communication and less prone to circumlocutions and Victorian adornments of speech. So, this may well be part of a general development, but what about its roots? What caused these cultural changes? I am no wiser.

      This personal rapture was set off by perusing the 2010 issue of the Annual Review of Microbiology. It struck me that the articles I read were especially well written. I call as witnesses a few reviews by people I know. These include pieces by Kim Lewis (Persister Cells), Eric Rubin (and Michael C. Chao, Letting Sleeping dos Lie: Does Dormancy Play a Role in Tuberculosis?), and one by that master colorist of the microbial literature, Kevin Young (Bacterial Shape: Two-Dimensional Questions and Possibilities). Read and see for yourself.

       Editors’ Note: We received the following response from Michael Yarmolinsky.

       On the Quality of Scientific Writing

      by Michael Yarmolinsky

Truth and clarity are complementary *

      — Niels Bohr

      Elio, in a posting of September 16, 2010, comments on the improved quality of scientific writing (in the literature of microbiology). Simple declarative statements are found in greater abundance; the passive voice is no longer used to avoid the first person; the titles of articles are more likely to come to the point and unlikely to be part of a numbered series; and humor is permitted. An examination of the implications and possible causes of the “changes in culture (sensu lato)” that Elio views with approval may interest, and perhaps surprise, the readers of this blog.

      With respect to the declining use of the passive voice, one cause should be obvious. It is the insistent attention bestowed on sentences in the passive voice by grammar and spell check programs. Do not let a misguided word processor intimidate you. The impersonal style in expository writing is entirely appropriate. Your processor may underline “bacteria were grown in LB,” but do not replace it with “I grew the bacteria in LB,”(Do indicate whether the recipe called for 5 g/l of NaCl or 10 g/l. It can make a difference.)

Elio cheerfully notes that titles have become more informative. The abruptness and magnitude of the change is astonishing. A shift in the style of titles, from the indicative (denoting the subject) to the declarative (asserting that something is so) was documented in 1990 by J L Rosner.¹ Of 2582 titles published in the Proceedings of the National Academy of Sciences from 1960 to 1969, not one is a declarative title, but by 1980 25% were declarative and