In the Company of Microbes. Moselio Schaechter

it was hoped—and rigorously asserted by its practitioners—that living systems could be completely understood in terms of the properties of their constituent parts (fundamentalist reductionism), and biology ultimately would be reduced to physics, as according to James Watson: “... there are only atoms. Everything else is merely social work.” Evolution research was dismissed because, being in essence historical, it could not be reduced to physics. Instead, the fitting approach was to solve the structures of biomolecules, which would thereby reveal their function. Likewise, the road to increased understanding of biology was the falsifiable working hypothesis, itself derived from previous experimental results (empirical reductionism).

      Influenced to some extent by the New Age idea that our planet is most fittingly perceived in toto as a single living organism, a growing number of biologists in the ’80s began to argue for a holistic approach. The reductionist approach then in vogue could not explain the emergent properties of complex biological systems, or, as Steven Rose phrased it: “...watch a flock of birds, startled by a noise, take off from the field on which they have settled—see them wheel and turn in formation, and try to explain or predict the behaviour of the group merely from a knowledge of the wing-musculature of each individual and aerodynamic theory.” However, there was a flaw in this argument: no holistic concept at that time was able to propose meaningful experiments.

      At about the same time, a second criticism was put forward by biologists concerned that reducing biology to physics could in the end strangle scientific creativity. They favored curiosity-driven research over technology-driven research. Or, as Elio put it during a meeting in ’87 in memory of Luigi Gorini: “On the planet Krypton every experiment works. As a consequence people quickly run out of ideas and so they spend their time sequencing the human genome. With Luigi, experiments did not always work, but he never ran out of ideas.”

Now, early in the twenty-first century, the situation is dramatically different. Never before were the life sciences explored by so many researchers from diverse cultural backgrounds, both men and women. Due to the ever-increasing speed of technological development, research now spans about five rather than three contemporary generations. Cutting-edge technology of the ’80s is at best of historical interest today—who remembers Maxam-Gilbert sequencing? Experiments have become less tedious, but they now produce so much data for analysis that hardly any time is left for any of these multiple generations to debate what it all means. When the human genome sequence was published, biology hit a wall of biological complexity. Many biologists saw that fundamentalist reductionism was failing and the spiral of progress arrested as biology was drawn in various directions. Its central narrative seemed lost—almost.

      At this point, enter the paper by McFall-Ngai et al., just in time, adding umami flavor to Carl Woese’s call for “New Biology for a New Century.” That call was paraphrased elegantly by Freeman Dyson: “... postulating a golden age of pre-Darwinian life, when horizontal gene transfer was universal and separate species did not yet exist. Life was then a community of cells of various kinds, sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. ... But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell separated itself from the community and refused to share. Its offspring became the first species of bacteria—and the first species of any kind—reserving their intellectual property for their own private use. With their superior efficiency, the bacteria continued to prosper and to evolve separately, while the rest of the community continued its communal life.” Although Margaret McFall-Ngai and her co-workers refrain from expressing it explicitly, I can easily imagine them adding to this narrative: ...In separating itself from the community, refusing to share everything, this first species did not end communication with its siblings and the rest of the bunch, but rather increased its specificity, as witnessed by the ubiquitous communication among and direct interactions—even gene swapping—between the extant prokaryotes and eukaryotes, viruses, and a plethora of mobile genetic elements.

      The sequence of the E. coli rrnB gene determined in 1979 by the Maxam-Gilbert technique.

To come full circle—or more precisely to reenter the spiral—Karl Popper had suggested already in 1986 that by adopting “active Darwinism” biology would avoid the teleological trap and eventually come into accordance with his scientific method of reductionism. Instead of the prevailing view in which selection was the imposed driving force of evolution, Popper’s “active Darwinism” proposed that: “...the organism itself is not passive and neutral, waiting to be selected, but instead actively participates in its own selection, by choosing appropriate environments and modifying inappropriate ones; organism and environment interpenetrate and modify one another in ways which are determined in part by their own mutual history.” I assume Margaret McFall-Ngai and her colleagues would prefer the plural here: organisms and environment interpenetrate and modify one another... This added complexity can then be tackled by the approved methodologies of empirical reductionism without the danger of reverting to “stamp collecting,,” as pointed out by Carl Woese.

      This is where we stand today. Biology has its twenty-first-century narrative, which is just another word for an extended to-do list for biologists. The good news (for Elio, in particular): acute observation and curiosity have regained their pivotal role in finding out what life is all about. As we move forward, we eventually can teach computers one of the most precious, though enigmatic, of human traits—pattern recognition—so they can help us to cope with the approaching tsunami of data, help us visualize biological complexity.

      Christoph Weigel is a lecturer in Life Science Engineering at the Hochschule für Technik und Wirtschaft, Berlin, Germany, and an Associate Blogger.

       References:

      McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. 2013. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA 110:3229–3236.

      Rose S. 1988. Reflections on reductionism. Trends Biochem Sci 13:160–162.

      Woese C. 2004. A New Biology for a New Century. Microbiol Mol Biol Rev 68:173–186.

      June 10, 2013

       bit.ly/1RYA8SO

      #115

      by Elio

      Is global warming likely to result in a significant net increase, decrease, or no substantial change in the microbial biomass on Earth?

      December 3, 2014

       bit.ly/1hOOeoO

PART 2

      Accounts of the Past

      As science advances, stellar research of the day fades from the spotlight. Here I retrieve a few examples from the good old days.