2015 Annual Science Report

University of Illinois at Urbana-Champaign Reporting  |  JAN 2015 – DEC 2015

Project 2: Cells as Engines and the Serpentinization Hypothesis for the Origin of Life

Project Summary

All life is, and must be, “powered” since all of its most essential and distinguishing processes have to be driven “up-hill” against their natural thermodynamic direction. By the 2nd law of thermodynamics, however, a process can only be made to proceed up-hill by being mechanistically linked, via a molecular device functioning as an engine, to another, more powerful, process that is moving in its natural, down-hill direction. On fundamental principles, we argue, such engine-mediated conversion activities must also have been operating at, and indeed have been the cause of, life’s emergence. But what then were life’s birthing engines, what sources of power drove them, what did they need to produce, and how did they arise in an entirely lifeless world? Promising potential answers to these and other questions related to the emergence of life are provided by the Alkaline Hydrothermal Vent/serpentinization (“AHV”) hypothesis, whose original propounder and lead proponent, Dr. Michael Russell of JPL, is a co-investigator on this project. The goal of the project is specifically to clarify the essential mechanistic modus operandi of all molecular engines that power life, and to see how the most fundamental and prerequisite of these could have arisen, and operated, in the structures and flows produced by the serpentinization process. Importantly, candidate answers to these questions can be put to definitive laboratory tests.

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

Interest in the AHV/serpentinization model for the emergence of life derives mainly from the fact that the alkaline vents produced by serpentinization acting in an ocean floor can generate precipitate structures that are seemingly ideal incubators for life’s genesis. Comprised of immense labyrinthine arrays of mineral-membrane-bound microchambers, these structures, in the Hadean epoch, would have formed a kind of abiotic stromatolite whose “cells” were richly supplied by the operating geochemistry, and thus “for free”, with a full-fledged ambient, transmembrane protonmotive force and a suite of life-appropriate redox gradients – and thus could have functioned as minimalist “mineral-mitochondria”. Further, the membranes of these mineral-mitochondrial cells husband specific transition-metal sulfide and oxyhydride complexes (closely comparable to some of the active centers of modern enzymes doing similar work) could then have enabled molecular engines capable of coupling the external, geochemically-given disequilibria to the internal endergonic reactions necessary to initiate the emergence of life: e.g. the production of pyrophosphate (the precursor to ATP as a free energy carrier) from orthophosphate and the fixation of carbon from CO2 and of nitrogen (as ammonium) from nitrate. No “soup” this, but a highly dynamic and organized, and self-organizing, engine-powered rocket ship; one which, in one place and time, achieved “ignition” and then, autocatalytically, lifted off – bringing the planet to life.

The challenge, of course, is to prove it; and the key step is to catch the proposed abiotic engines in the act. Efforts to address this challenge are now underway at a number of centers (e.g., UC London and the RIKEN Center, Japan), but are somewhat hampered, we believe, by confusion regarding how molecular engines, i.e. processes that can convert one disequilibria (e.g. a redox gradient) into another (e.g. fixed carbon) actually function. It is widely held that these processes are just (electro) chemical reactions, and that therefore what we need find in the abiotic world are catalysts that can mediate these reactions. But this is incorrect; such processes are not just chemical reactions, and they need devices to mediate them that are not just acting as catalysts. What they require are true molecular engines.

Our work with Michael Russell over the last few years, the last year in particular, has focused in large part on an effort to explicate this specific issue, and to use that understanding to guide experimental attempts at model validation. The essential point at issue is that molecular engines are fundamentally Brownian ratchets controlled by an escapement mechanism. The escapement’s purpose is to ensure that an instance of the driven, up-hill reaction, itself produced by Brownian fluctuations, “gates” (i.e. allows to go to completion) an instance of the quasi-irreversible driving reaction; this then “traps” the driven reaction, in effect permitting only favorable (i.e. “rectifying”) Brownian fluctuations in a 2nd-law consistent manner, and allowing work to be done. We have recently developed a conceptual and statistical-physics model of such escapement-mechanism-mediated disequilibrium conversion processes. We argue that this model can stand as a “Turing Machine” abstraction, capturing, in their simplest possible realization, the essential and universal features of all molecular engine devices – and which, thereby, describes an enabling, and indeed universal, property of life.

Our most recent work, organized around the non-equilibrium thermodynamics involved in disequilibria conversion, and the role of molecular escapement mechanisms was, in an early form, was first presented in November 2014 by Branscomb (co-author Russell), at the TDE Focus Group meeting at ELSI in Tokyo. The first paper to be based on it, (Escapement Mechanisms and the Conversion of Disequilibria; the engines of creation. E. Branscomb , T. Biancalani , N. Goldenfeld and M. Russell), a substantial work with nearly 200 literature citations, was submitted for publication to “Royal Society Open Science” at the end of 2015, though that journal felt that it was not of an appropriate type for their publication and declined to review it. The paper is now being slightly rewritten and will be resubmitted in approximately a month’s time. Two direct follow-on papers are also in preparation. The first assesses the validity and generality of the claims made in the first paper by comparing them against a substantial list of biological free energy converting systems for which mechanistic models have been proposed. This paper was the subject of poster presented at the recent GRC Origins of Life conference in Galveston: “Fluctuation relations, bioenergetics, and the emergence of life”, by E. Branscomb and M. Russell. In the second we discuss specifically the implications of the first paper’s arguments for the question of what conditions are necessary to engender life on a lifeless planet, and therefore, what kinds of experimental tests should be conducted to resolve the question. We believe these two papers will be ready for submission within the first half of 2016.

In June 2015 I, along with Goldenfeld, Biancalani, and Russell attended the AbSciCon meeting in Chicago at which I presented our poster on the stat-mechanical model of disequilibria.

Figure 1. Escapement-controlled Brownian engines; how molecular disequilibria are “converted”; a model disequilibrium-converting engine illustrating the universal principles governing disequilibria conversion (often mis-called “energy conservation” in biochemistry). Here the disequilibria are simple concentration differences between left and right halves of a box divided by a partition having a portal through which particles can pass one at a time. Two such boxes, arranged vertically, are presented, one with blue, one with red particles. The passage of particles through the portals is controlled by an oscillating gate, in that only when the gate is open to one side or the other can a particle enter or leave the portal space. The two gates are linked mechanically so that they oscillate between open-left and open-right together. Both the motion of the particles and the oscillation of the coupled gating mechanisms are driven by thermal fluctuations. However, thermal fluctuations that would flip the gate between its two orientations are blocked from having that effect unless both top (blue) and bottom (red) portals are filled with particles (with no bias as to direction). This rule makes the gating mechanism into an escapement and the entire system into an engine. In the figures, the system is shown on the left in a presumed starting configuration in which the top chamber is in maximum disequilibrium and the bottom chamber in approximate equilibrium. As the system is allowed to operate (again, merely as driven stochastically by thermal fluctuations), it evolves to a steady state configuration, as illustrated by the right hand figure, in which the upper (the driving) disequilibrium is partially relaxed and a partial disequilibrium has been created in the lower (driven) chamber. All “energy conserving” systems in biology operate in a manner consistent with the principles illustrated by this simple paradigmatic model.

  • PROJECT INVESTIGATORS:
    Elbert Branscomb Elbert Branscomb
    Project Investigator
  • PROJECT MEMBERS:
    Tommaso Biancalani
    Co-Investigator

    Nigel Goldenfeld
    Co-Investigator

    Michael Russell
    Co-Investigator

  • RELATED OBJECTIVES:
    Objective 1.1
    Formation and evolution of habitable planets.

    Objective 1.2
    Indirect and direct astronomical observations of extrasolar habitable planets.

    Objective 3.1
    Sources of prebiotic materials and catalysts

    Objective 3.2
    Origins and evolution of functional biomolecules

    Objective 3.3
    Origins of energy transduction

    Objective 3.4
    Origins of cellularity and protobiological systems