Protocell autonomy: linking processes through self-made boundaries / ‘Avtonomija protocelic’: povezovanje procesov s samoustvarjanjem meja

author: Kepa Ruiz-Mirazo, Department of Logic and Philosophy of Science, Biophysics Research Unit, University of the Basque Country
published: Oct. 21, 2011,   recorded: October 2011,   views: 122
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Autonomy does not mean independence. It refers, rather, to the capacity of a system to define its own rules of operation as such a system, including the rules of interaction with its environment. This applies to biological systems which are able to build their boundaries (lipid membranes) and other functional components (proteins, sugars, nucleic acids, etc.) through the transformation of externally available material and energetic resources. They manage to do so by putting together and coordinating (both spatially and temporally) a complex network of reaction processes that take place in non-homogeneous, far-from-equilibrium thermodynamic conditions. Thus, biological systems, being necessarily open systems, constitute a dynamic organisation of processes that becomes clearly distinct from the inert environment that nurtures them and, at the same time, collects the products of their ongoing activity. In this article, I will argue that autonomy, in its most basic and minimal sense, had to be developed quite early in the sequence of transitions that led from complex physicalchemical systems to the simplest biological ones. Apart from relevant experimental evidence provided in present days by several labs, a theoretical model will be introduced to show how this could be achieved: namely, through the coupling of autocatalytic chemical reaction networks with processes of lipid self-assembly forming the membrane of the system. This marks an important transition, in which »vesicles« (closed bilayers) transform into »protocells «, for they gain control on the production of their own boundaries, a crucial step for autonomous individuation and system-level regulation. The idea will be illustrated both for protocells made with various types of lipidic molecules, some of which are internally synthesized (Fig. 1), and for more complex cases in which lipids are combined with oligopeptides (Fig. 2), bringing about a richer space of dynamic and regulatory behaviours. Accordingly, lipid boundaries will not be portrayed as barriers, as molecular structures that serve for separation or disconnection with the surrounding milieu but, rather, as linkers of processes: i.e., as the organic interfaces in which diverse mechanisms to control energy-matter flows are anchored, making actually possible the continuous constructive dynamics of biological systems. The complementary relationship between boundaries and internal network of reactions will be, therefore, highlighted, following the steps of the autopoietic theory, but giving a more physically grounded and updated interpretation of the idea. Furthermore, autonomy will be claimed as a necessary but not sufficient theoretical construct to account for living phenomena, whose evolutionary-historical-collective dimensions also need to be taken specifically into account.


Avtonomija ne pomeni neodvisnosti. Namesto tega se nanaša na sposobnost sistema, da določi svoja pravila delovanja, vključno s pravili interakcije s svojim okoljem. To velja za biološke sisteme, ki so s preoblikovanjem razpoložljivih zunanjih materialnih in energetskih virov sposobni zgraditi svoje meje (lipidne membrane) in druge funkcionalne sestavine (beljakovine, sladkorje, nukleinske kisline itd.). To uspejo s časovnim in prostorskim povezovanjem in usklajevanjem kompleksnih mrež reakcijskih procesov, ki potekajo v nehomogenih, neuravnovešenih termodinamičnih pogojih. Tako biološki sistemi, ki so nujno odprti sistemi, predstavljajo dinamično organizacijo procesov, ki so jasno ločeni od inertnega okolja, in sočasno zbirajo produkte svojih dejavnosti. V tem prispevku trdim, da se je avtonomija v svojem temeljnem in ozkem smislu morala razviti precej zgodaj, skozi zaporedje prehodov, ki so vodili od zapletenih fizikalno-kemijskih sistemov k, biološko gledano, najenostavnejšim sistemom. Poleg ustreznih eksperimentalnih dokazov, ki so jih že zbrali v različnih laboratorijih, predstavljam še teoretični model, ki prikazuje, kako pride do prehoda od fizikalno-kemijskih k živim sistemom: s pomočjo sklopljenja mrež avtokatalitičnih kemičnih reakcij s procesi samozdruževanja lipidov, ki tvorijo membrane sistema. To zaznamuje pomemben prehod, pri katerem se «mehurčki» (vezikli, zaprti dvosloji) preoblikujejo v «protocelice », ki pridobijo nadzor nad proizvodnjo svojih lastnih meja, kar je ključni korak za avtonomijo in regulacijo na ravni sistema. Idejo prikazujemo tako za protocelice, ki so zgrajene iz različnih tipov lipidnih molekul (nekatere od njih se sintetizirajo interno; slika 1), kot za bolj kompleksne sisteme, v katerih poleg lipidov nastopajo še oligopeptidi (slika 2), kar obogati, in razširi nabor dinamičnih in regulacijskih vedenj živega sistema. V skladu s tem lipidnih meja ne prikazujemo kot ovire (na primer kot molekularne strukture, ki služijo za ločitev od okolice), ampak kot povezovalce procesov: kot organske vmesnike, v katerih se nahajajo različni mehanizmi za nadzor energetskega pretoka, kar dejansko omogoča stalno konstruktivno dinamiko bioloških sistemov. Zato poudarjamo pomen komplementarnega razmerja med mejami celice in notranjim omrežjem reakcij, pri čemer sledimo avtopoietični teoriji, a obenem podajamo interpretacijo na fizikalni osnovi. Poudarjamo, da je avtonomija nujen, vendar ne zadosten teoretični konstrukt, da bi upoštevali vse življenjske pojave, ki jih iz evolucijsko-zgodovinsko- kolektivne dimenzije ne smemo spregledati.

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Download slides icon Download slides: bzid2011_ruiz_mirazo_protocell_01.pdf (4.0 MB)

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