Con el tiempo, estos Mapas Desmesurados no satisficieron y los Colegios de Cartógrafos levantaron un Mapa del Imperio, que tenía el tamaño del Imperio y coincidía puntualmente con él. Menos Adictas al Estudio de la Cartografía, las Generaciones Siguientes entendieron que ese dilatado Mapa era Inútil y no sin Impiedad lo entregaron a las Inclemencias del Sol y los Inviernos.
Jorge Luis Borges, Del Rigor en la Ciencia, 1946 A big part of our research program has been centered in understanding the rules that govern the assembly and function of microbial communities. To this end, we study communities that form in the lab under well controlled conditions in synthetic environments. This offers many advantages, perhaps most notably that we can alter the external environmental conditions in which assembly takes place, the diversity and composition of the initial inoculum, the degree of connectivity between habitats, the rate of nutrient and energy inflows, etc. The ability to control the environment is critical if we wish to tease apart questions such as how do multiple different environmental nutrients contribute to community composition, how temperature affects the taxonomic structure of microbial communities, or whether simple pairwise assembly rules may capture coexistence in a complex community. A common critique we have received, as a weakness of this strategy, is that our experiments are conducted under artificial conditions, and therefore they represent just a “toy model” for the real world. Over the years, I have given several responses to this critique, which I would like to share in case they are useful to others. The first one is that there is nothing wrong with toys! Toys can be extremely useful devices to help us figure out laws and principles of nature. Toys like pendulums and springs play a prominent role in physics. They were instrumental to figure out the the very same laws that, to first approximation, govern the motion of planets and all other naturally occurring objects. One could argue that microbial consortia grown in the lab may also be used to inquire about the existence of general rules and principles in microbial ecology. It is certainly fair to ask whether the rules that govern the stability, productivity and function of lab-grown microbial consortia should fundamentally differ from those that shape natural microbial ecosystems, whose scale, diversity, environmental complexity etc. are much larger. I do not know the answer yet. Many times in science “more is different”, and it is very possible that the principles that govern low-diversity consortia will in fact differ from those that shape natural ecosystems. But precisely to that point, studying how exactly they differ is an enormously important question. If such fundamental differences exist as the system grows in scale and diversity, isn’t it worth identifying and understanding how and why? The second response is practical in nature: microbial communities grown in artificial, man made environments such as fermentors can have enormous biotechnological potential, as many have argued before. These artificial microbial consortia are ecological communities in their own right, as legitimate a system of study (and as worthy of our attention) as any other in ecology. Just their practical utility alone makes a good case for why studying such artificial microbial consortia is in fact very relevant, even if it were true that the lessons one learns by doing so do not translate in an obvious manner to natural microbial ecosystems. Related to this response, I would also argue that studying the ecology of biotechnologically useful consortia can lead to theory whose applications extend well beyond the realm of artificial systems. The laws of thermodynamics were discovered largely by scientists studying engines, pistons, and other industrial devices at the dawn of the industrial revolution. The gases that one finds in these settings are far more controlled than those that form, say, the clouds in the sky. Yet, the thermodynamic principles that rule both of them, at equilibrium, are the same. Remarkably, thermodynamic laws reflect relationships between emergent properties of systems containing many particles. For example, the law of Guy Lussac describes the relationship between the pressure and temperature of a gas at constant volume in equilibrium. Are there similar relationships between emergent ecosystem properties? Even if one is of the persuasion that such laws do not exist, isn’t it worth putting the effort in making sure? Microbial consortia studied in the lab are ideal systems to search for the relationships between emergent properties as, similar to engines and pistons, they allow for a fluid dialog between theory and quantitative experiment. While I draw from physics quite a lot in the previous examples, there is also plenty of precedent in biology for studying microbial consortia under artificial conditions. A lot of what we know about proteins and protein function was figured out by isolating proteins from their “natural environment” (e.g. the cytoplasm of a cell) and placing them under well controlled laboratory conditions that could be manipulated and their effect unambiguously monitored. The fields of enzymology, protein folding, molecular motors, etc. have their foundation on such experiments. I often argue that the interior of a cell, from the perspective of a population of proteins, may not look much less complex than an ecosystem does from the perspective of a population of individuals. Is there a solid argument why such a reductionist approach is reasonable for proteins but not for microbial cells? I am aware of the many limitations of synthetic consortia, and the dangers of over-generalizing from such a system. A microbial consortium formed in the lab is not meant to be a wet-simulation of the soil microbiome, let alone of guppies in a stream, or hippos in the savanna, and extending the lessons learned from one to the other is far from straightforward. There is strong evidence that the functions of microbial consortia are highly sensitive to the environment, and a consortium that exhibits a particular function in the lab should not be trivially expected to maintain it if we simply spray it onto, say, the leaves of a plant. While being cautious in this regard is definitely a good idea, this does not argue against reductionism altogether. The lessons learned from reductionist experiments in protein biochemistry can and have been challenged by later studies. Chaperones were not present in the initial Anfinsen experiment, and many proteins require them to fold properly. While Anfinsen's dogma was later qualified, few would now argue that it was not a critical step in the field. Moreover, the study of chaperones has also benefited from in vitro experiments, arguing for their continuous relevance to modify incomplete pictures. Similarly, synthetic communities lacking a particular element, like phages, protists, or spatial structure, may give us an incomplete view of the assembly process, but this is not a lethal flaw. Rather, I would argue that it is an advantage as, by construction, synthetic microbial communities allow for the systematic addition and removal of different components of a natural microbiome. In sum, I argue here that studying microbial communities under well controlled, artificial laboratory conditions may be as fruitful and useful as similar reductionist approaches have been in other areas of science, both in biology and beyond. The key question is not whether they should be studied or not, for the answer I argue is yes, but rather "what do we use them for". Nobody I know who studies microbial communities in the laboratory is under any delusions that their low-diversity consortia grown under stable laboratory conditions are a faithful representation of "the real thing in nature". Attempting to reconstruct the soil or the human gut in the lab is practically impossible, and it may be pointless too. No matter how many components and details one adds, any laboratory system will never be "the real thing", as some detail or another will always be missing. As in the famed Borges story, only the real thing is "the real thing". If one is able to capture essential features of an ecosystem under highly artificial conditions, this is a massive step forward. But I would argue that the main use of synthetic communities is not to simulate a particular ecosystem. Rather, it is to find general principles that rule community assembly and community function. Artificially assembled communities not only offer an excellent testing ground for theory, but they also have practical utility of their own. They are an essential component of the scientific process in microbial ecology, which also includes of course observational and manipulative studies of natural communities in their natural habitats. If rules and generalities exist, and we wish to find them, studying artificial communities is a necessary step.
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