Most of the literature on the origin of life is based on the bottom-up approach, namely starting from low molecular weight prebiotic compounds, or from an initial prebiotic single species like RNA, followed by an escalation of structure and functionality. It is argued against such an approach that has brought no real clarification to the core question, i.e., how life has originated from non-life. It’s argued in favor of a change of the initial paradigm, namely in favor of a top-down approach, particularly starting from a chaotic mixture of vesicles containing already both nucleic acids and polypeptides. The basic assumption here is the existence of prebiotic pools of nucleic acids and/or polypeptides. The recent finding that RNA spontaneously forms on basalt lava glass, which was abundant on Earth 4.35 billion years ago5, is taken to give support to the existence of prebiotic pools of nucleic acids. A chaotic ensemble of vesicles containing all possible configurations of nucleic acids and polypeptides may give rise, thanks to principles of selection, to a small family of filled vesicles that can have the right order of macromolecular components to initiate the pathway towards primordial cellular forms.
The concept of order out of chaos is nowadays accepted. A well-known case, also epitomized by the last Nobel Prize to Giorgio Parisi, and which is often under our eyes, is the regular geometrical forms of migrating birds in our sky. Regular order is not due to a leader animal that is in flight, but to a spontaneous aggregation due to short-range interactions, each bird sensing only the presence of a few near neighbor interactions1. The work of Prigogine and coworkers2, in a broader context, has paved the way for a scientific approach to this phenomenology.
It is the short-range interaction among near-neighboring elements which gives rise to a new equilibrium that, finally, involves the whole system, a new equilibrium that may assume the morphology and the physical properties of a new, unexpected deterministic species.
Now, let us turn to the problem of the origin of life. It is a vast field, born about one century ago with the classic little book of Oparin3, and his preface is worthwhile reading even now, almost one hundred years later. But it is the basic ontology that is important: Oparin was influenced by the dialectic Marxism and by the Darwinism at the same time and therefore he was ascribing the origin of life to a natural process starting from ground zero-obviously excluding any divine interference. This concept gave rise to the bottom-up approach. Accordingly, all started from small simple molecules, that with time and due to physical forces, were capable of associating, forming structures more and more complex, whereby the increase in complexity was also yielding an increase in functionality, till the formation of the self-replicating cells.
In all these bottom-up scenarios, complexity is formed from simplicity. Actually, this way of thinking is the most obvious in our mind, probably it is even one of the archetypes of C.G. Jung's memory. After Oparin, several things happened, the most important being the famous experiments of Stanley Miller in 19534. This work gave reinforcement to the pristine idea that also the complexity of life can be obtained from lower simple components.
Not that anybody has ever really described the molecular steps leading from low molecular weight compounds like pristine amino acids, or from a primordial RNA to living cells. And nobody, until now, has created in the lab a cell from scratch, and in this regard, it is not improper to recall here, that life on this Earth is only cellular-no other forms of life is known. And if you want to make life, you need to reach the level of a cell-or better, a colony of cells. We don’t know how to do this. The field of the origin of life is actually an active field, with many beautiful papers from the scientific point of view. But if you ask, which of these papers has really to do with the question "how did life arise from the non-living world?" you would be deluded. Therefore, to this day, the honest answer of any scientist to the question "how did life arise on our planet?" remains: I do not know.
A recent paper that was circulating5, describes a new pathway for the biogenesis of RNA. This is indeed, per se, a nice important discovery. I welcome particularly this finding, as I have in the last years been advocating prebiotic pools of nucleic acids6, as we will see shortly. The authors take this finding as almost equivalent to the origin of life, but this jump from a single molecular species to the complexity of cellular life is completely gratuitous. RNA as a molecular species is not a novelty, it has been around and at disposal of all molecular biologists for so many years, and no one has come up with a concrete pattern describing how you go from RNA to cellular life. We have again a repetition of the old paradigm, that life may originate from a single molecular species, without saying how namely again with the naivety and self-referentiality of the bottom-up approach. Elsewhere6, I have suggested that the fact that the origin of life is still a mystery. It might be due to our inborn paradigm, namely the bottom-up approachb, and to our luck of alternative ways of thinking.
b. Not that I have been always against this approach. For several years I was supporting the notion of the minimal cell, with the very first papers7 on this field based on the bottom-up approach: how by adding one protein and or one nucleic acid species at a time into a liposome, you might be able to arrive at the minimal cell, namely, a cell containing the minimal and sufficient macromolecular components to be defined as living. The basic idea, here too, was that the complexity of modern cells-hundreds of genes- must have been preceded by some kind of minimal cell, possessing very few genes. Nice idea, nice papers, but mostly due to these several years of work, I had to change my mind, seeing how such a project was impossible from both the practical and the conceptual viewpoint. Arriving to reject the bottom-up approach as the logical pathway to life6.
The top-down approach
Now let us go back to our birds forming perfect geometrical forms, given as an example of how order may come out of an initial chaotic condition.
Is there a way to present a perspective of this kind for the origin of life?
One theoretical possibility is to start from a situation in which there is an abundance of already made macromolecules. Let us say pools of proteins and nucleic acids. Obviously, there is no evidence yet that large pools of DNA and of proteins existed in prebiotic times.
However, the recent paper by Steve Benner and collaborators indicates that RNA spontaneously forms on basalt lava glass and that such glass was abundant on Earth 4.35 billion years ago5. To assume that also DNA was present in prebiotic times is not a complete fantasy.
Figure 1. Some TEM micrographs showing the macromolecular overcrowding were collected mostly by Pasquale Stano and Teresa de Souza (see 11,12).
Also, one should take into account that already 4 billion years ago, or shortly after, apparently there were a lot of unicellular organisms on earth, and the question should arise: where did all the corresponding DNA, and proteins, came from? (We have now on Earth about 50 billion tons of DNA -hard to believe, isn't?8).
Following the gist of the speculation about the prebiotic existence of pools of DNA and proteins, how to proceed further? Is it possible for example to compartmentalize these macromolecules into vesicles? Not only simple compartmentalization, but we need a high local concentration, as it is well known that living cells are not diluted water solutions, but rather highly local concentrations of macromolecules.
We have some good recent experimental indications that this type of compartmentalization is possible. In particular, the following has been documented9-12: given a dilute solution of macromolecules, and adding then a vesicle-forming surfactant, like for example fatty acids, the closing of the surfactant to make a vesicle, acts as a non-linear attractor. In this sense, the final distribution of macromolecules in the vesicles doesn’t follow an expected Poisson-like mode, but there is rather an all-or-nothing situation, with a lot of empty vesicles (not-containing macromolecules or only a few) and a few vesicles which are instead overcrowded. Namely, a local concentration that can be up to two orders of magnitude higher than the original diluted protein solution.
Typical data are shown in Fig.1. The over-crowding effect holds for various macromolecular species, not only for ferritin but for other biopolymers, including ribosomes10-12. Kinetic and thermodynamic factors are probably responsible together of this effect, but a clear explanation is still missing.
The fact that a high local concentration permits biological reactions which are not possible in a dilute environment is well understandable, and it has been beautifully demonstrated by diluting a commercial in vitro-protein synthesis preparation, to obtain no viability. Then adding a vesicles-forming surfactant, thus recovering viability12.
Also, the whole Ueda system13 consisting of ca. 90 macromolecular species can be incorporated by this technique into vesicles11-12 permitting the biosynthesis of the green fluorescent protein inside the vesicles.
The net result of fig.1 is rather clear and important: given a diluted solution of biopolymers, the production of vesicles in situ is going to produce spontaneously vesicle compartments having a high concentration of reagents – so as to possibly permit interactions and reactivity which are not possible in a diluted solution. Although the number of overcrowded vesicles is much smaller than the empty ones, even if there are only 0.1% of them, their sum amounts to billions. And they will differ from each other stochastically in terms of distribution and relative concentration of the reagents. So many, that one is tempted to use the arguments of the anthropic principle14. You may remember this argument, according to which there are many parallel universes, each one with its own universal constants-so many, that there is even one in which the emergence of life is possible (and we happen to be in this one). But aside from the anthropic principle, and aside from the tiny probability of a magic start, let us see some basic features of this new platform to study the origin of life.
A New Starting Platform
Vesicles containing nucleic acids and /or proteins are not the solution to the origin of life. There is no doubt however that starting from a chaotic top, where we have already so many vesicular forms containing macromolecules, new vistas and perspectives are possible. Mostly, we are dealing with a new starting platform away from the simplistic bottom-up approach which I consider the reason for the stillstand in the field of the origin of life. And, the finding of Benner and coworkers, rather than being yet another way to start again with a bottom-up approach, in my opinion, is the one that gives strength to this new platform. Abandon the bottom-up mentality and look at new ways to arrive at the origin of life.
Several preliminary questions come to mind with the new starting platform, for example, which kind of nucleic acid, which kind of prebiotic proteins, can one envisage at the start? And, which are the selection steps that may bring the chaotic ensemble of billions of stochastically different vesicles towards an ordered smaller ensemble? Here comes the individuality and fantasy of each investigator.
I am thinking for example the work of Kenjii Ikehara15, who has been advocating an origin of life-based on the poly-condensates of GADV, namely Glycine, Alanine, Valine, glutamic acid (D), which were abundant in prebiotic time-although he also, as most other authors, operates with the bottom-up approach.
The main message of this article is simply to propose a new platform, a totally different way, to study the origin of life. Starting from a large initial complexity, and proposing to possibly utilize the principles of selection, to reach a macromolecular configuration capable of directing our steps towards the formation of (colony of) cells, that are the only signature of life on this Earth.
1 Viana, D.S., Santamaria, L., Figuerola, J., Migratory Birds as global dispersal vectors, 2016, Trends in Ecology, 31 (10) 763-775; Somvveille, M., Manica, A., Butchart, S.H.M., Rodriguez, A.S.L., 2013, Mapping global diversity patterns for migratory birds, PlosOne, Aug.; see also YouTube under regular patterns of migratory birds.
2 Prigogine, I., and Stenger, I.1984, Order Out of Chaos, Bantam publ.
3 Oparin, A. I. (1924). Proishkhozhddenie Zhisni. Moskowski Rabocii; (1957). The Origin of Life on Earth, 3rd edn., Academic Press.
4 Miller, S. L. (1953). Production of amino acids under possible primitive Earth conditions.
5 Biondi, E., Jerome, C. A., Kim, H.-J., Mojzsis, S. J., Benner, S. A. (2022) Catalytic synthesis of polyribonucleic acid on prebiotic rock glasses. Astrobiology in press.
6 Luisi, P.L. 2020, “Why the Origin of Life is Still a Mystery”, J. Syst. Chem. 8, 1 – 8.
7 Oberholzer, T., Albrizio, M., and Luisi, P. L. (1995a). Polymerase chain reaction in liposomes. Curr. Biol., 2, 677–682.; Oberholzer, T., Wick, R., Luisi, P. L., and Biebricher, C. K. (1995b). Enzymatic RNA replication in self-reproducing vesicles: an approach to a minimal cell. Biochem. Biophys. Res. Commun., 207, 250–257.; Oberholzer, T., Nierhaus, K. H., and Luisi, P. L. (1999). Protein expression in liposomes. Biochem. Biophys. Res. Commun., 261, 238–241; Murtas, G., Kuruma, Y., Bianchini, P., Diaspro, A., and Luisi, P. L. (2007). Protein synthesis in liposomes with a minimal set of enzymes. Biochem Biophys Res Comm., 363: 12–17.
8 Riddihough, G., et al., Making RNA in the prebiotic world.
9 Luisi, P. L., Allegretti, M., de Souza, T. P., Steiniger, F., Fahr, A., and Stano, P. (2010). Spontaneous protein overcrowding in liposomes: a new vista for the origin of cellular metabolism.
10 Teresa de Souza, Stano, P., Steiniger, F., D’Aguanno, E., Altamura, E., Fahr, A., and Luisi, P. L. (2012). Encapsulation of ferritin, ribosomes, and ribo-peptidic complexes inside liposomes: insights into the origin of metabolism. Orig. Life Evol. Biosph.
11 Teresa de Souza, Fahr, A., Luisi, P. L., Stano, P. (2014). Spontaneous encapsulation and concentration of biological macromolecules in liposomes: an intriguing phenomenon and its relevance in origins of life. Journal of Molecular Evolution, 79, 179–192.
12 Stano, P., D’Aguanno, E., Bolz, J., Fahr, A., and Luisi, P. L. (2013). A remarkable self-organization process as the origin of primitive functional cells. Angewandte Chemie International Edition, 52, 13397–13400.; Murtas, G., Kuruma, Y., Bianchini, P., Diaspro, A., and Luisi, P. L. (2007). Protein synthesis in liposomes with a minimal set of enzymes. Biochem Biophys Res Comm., 363: 12–17.
13 Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., and Ueda, T. (2001). Cell-Free Translation Reconstituted with Purified Components. Nat. Biotechnol.
14 Barrow J.D. and Tipler F.J. 1986 The anthropic cosmological principle, Oxford Acad, Press.
15 Luisi, PL., 2016, The emergence of life, Cambridge Univ. Press.
16 Ikehara, K., 2021, Towards Revealing the origin of life, Springer.