Abstract
What is the relationship between evolution and autonomy, as conceived from the autonomous perspective? What role does history play? The general picture is that the evolution of biological systems stems from the mutual interplay between organisation and selection: in a word, organisation channels selective processes and selection drives organisation towards an increase in complexity.
This chapter elaborates on ideas previously presented in Moreno (2007), Ruiz-Mirazo et al. (2008) and Moreno & Ruiz-Mirazo (2009).
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Notes
- 1.
- 2.
We understand Salmon’s distinction as mapping onto Mayr’s one (more commonly evoked in the philosophy of biology) between “ultimate” and “proximate” causes (Mayr 1961). Accordingly, aetiological explanations would appeal to ultimate causes, while constitutive explanations to proximate ones.
- 3.
Recently, Rosslenbroich has developed an original account of the relations between autonomy and evolution (Rosslenbroich 2014). Although largely complementary, his account is quite different from ours in that it mainly focuses on the evolution of the physiological changes leading to what he calls an increasing “independence of the environment”. Accordingly, we leave a detailed analysis of his proposal for a future work.
- 4.
Actually, the concept of self-assembling mainly refers to the spontaneous formation of supramolecular (rather than purely molecular) structures in equilibrium or near equilibrium conditions.
- 5.
- 6.
Human beings are used to building, maintaining, and managing complex structures and organisations. This could lead us to think that the generation of complexity is not a big issue. Yet, whenever we try to make complexity develop in a scenario in which there is no human presence, nor any possible intervention of other living organisms, things become much less easy. This experience coincides with what happens in the natural world, where (with the exception of life) systems show no great organised complexity: self-organising phenomena, for instance, create some self-maintaining dynamic patterns but are unable to increase this minimal complexity, whereas certain assembling processes (like growing crystals) can generate and maintain a certain degree of structural complexity, but lack any form of functionality. Indeed, biological systems (and derivatively, human organisations such as social systems) constitute the only type of system we know of that can generate and increase both structural and functional complexity indefinitely.
- 7.
Even very simple template replicators may show “hereditary” variations. Think, for instance, of the case of a self-replicating crystal, which by chance incorporates a screw-dislocation. Since this dislocation speeds up the binding of ions, it preserves its screw structure as the crystal grows. But in order to display an evolutionary process, advocates of the “replication first” hypothesis require the presence of modular self-replicating templates, namely, replicators possessing sequences of different building blocks, whose hereditary modifications will be considered the key element for displaying an evolutionary process (see Sect. 5.5 below).
- 8.
Thirty years later, Oehlenschläger and Eigen (1997) showed that the Spiegelman monster eventually becomes even shorter, containing only 48 or 54 nucleotides, which are simply the binding sites for the enzyme RNA replicase.
- 9.
In terms of what the physical and chemical evolution of the universe can create in certain places during reasonable periods of time.
- 10.
To see why organisational closure is a crucial requirement for the increase of functional complexity, compare the situation above with that of a minimal dissipative structure, such as the flame. In this case, a variation of some component (the various material structures involved in the flow) does not affect the behaviour of the other, because it does not exert any specific causal contribution to the maintenance of the whole. Because of this, the flame will keep behaving in the same way in spite of various possible modifications of its components.
- 11.
A protocell is any experimental or theoretical model that involves a self-assembling compartment linked to chemical processes taking place around or within it. The model is aimed at explaining how more complex biological cells or alternative forms of cellular organisation may come about (Ruiz-Mirazo 2011). Here, we use the concept of protocell in a slightly more specific sense, as a compartmentalised closed system showing some lifelike properties, such as growth, autocatalytic activities, or reproduction (Rasmussen et al. 2008).
- 12.
Compartmentalisation could actually have induced self-reproduction. It might have been the case that, in some circumstances, chemical self-maintaining network developed within some, pre-existing available empty vesicles, so that the resulting system might have enlarged the vesicle until it slopped some of its chemical content over into a neighbouring vesicle; in turn, the chemicals could have slowly re-formed the original self-maintaining network (Hooker, personal communication). In this chapter, we do not discuss the specific conditions in which the reproduction of protocells might have emerged. We simply suppose that this step has been made at some point.
- 13.
For a detailed discussion of how a minimal form of functional diversity could arise in this scenario, see Arnellos and Moreno (2012).
- 14.
Szathmary (2006) has analysed the limitations of this form of pre-genetic mechanism of inheritance. We shall come back to this issue in next sections.
- 15.
In fact, current scientific research into the origin of life increasingly supports a synthetic view in which the three key questions – the formation of a proto-metabolic organisation, the creation of a selectively permeable compartment for this organisation, and its reliable hereditary reproduction – appear deeply entangled and therefore influencing each other (Ruiz Mirazo et al. 2013).
- 16.
Actually, it seems that quite small molecules could act as building blocks. For example, as shown by Manrubia and Briones (2007), certain small molecules of RNA can play the role of modules in a stepwise model of ligation-based modular evolution: RNA hairpin modules could have displayed ligase activity, catalysing the assembly of larger, eventually functional RNA molecules. These ligation processes allow a fraction of the population to retain their previous modular structure, and thus structural and functional complexity can progressively increase.
- 17.
A molecule acts as a template if its structure acts as blueprint, enabling the formation of copies of said structure. Modular templates (Maynard Smith and Szathmary 1995; Szathmary 2000) consist of interchangeable discrete units, which build up a specific one-dimensional sequence, and whose global three-dimensional shape is such that it allows the recurrent copying (by a chemical complementarity mechanism, like base pairing) of complete, equivalent sequences. Although modular templates are considerably complex molecules, simple kinds of templates probably played an important role in previous evolutionary stages.
- 18.
It is important to clarify that by “RNA world” we refer here not to “nude” self-replicating RNAs, but to closed organisations whose metabolism was catalysed by RNAs and whose reproduction was specified by RNA templates.
- 19.
RNA, however, cannot perform both functions in a very efficient way. We shall explain this point in the next section.
- 20.
Of course, this is not to say that during reproduction, inheritance mechanisms concern these templates uniquely, rather, that their importance lies in the fact that (1) they can “localise” the hereditary changes, and (2) they ensure the structural specificity of the most complex functional polymers of the system.
- 21.
The particular “performance” of a given metabolic organisation in a specific environment, and hence the capacity of this system to successfully reproduce, is dependent on the nature of the functional constraints that constitute this system. In this sense, selection operates on the organisation as a whole; but because (at least in certain cases) changes in hereditary records are linked to localised changes in functional constraints, selection could also be phenotypically specific.
- 22.
As Woese (2002) has pointed out, the beginning of cellular evolution was a collective process, where different cellular designs evolved simultaneously, systematically exchanging genetic material (what he calls “horizontal gene transfer”). So, this early (pre)Darwinian evolution would allow an exploration of different forms of organisation, until a “modern design” was reached.
- 23.
The current view of the origin of life postulates a stage of prebiotic systems based on a certain type of bi-functional polymers (like RNAs) capable of performing both template and catalytic functions, although in a much less suitable way than DNA and proteins. Hence, despite its evident limitation in the exploitation of both template and catalytic functions, this solution is organisationally much simpler (since it allows the direct conversion of a specific sequence into a specific catalytic task) and is therefore more likely to have occurred.
- 24.
This problem has a simple chemical interpretation. Template activity requires a stable, uniform morphology, suitable for linear copying (i.e., a monotonous spatial arrangement that favours low reactivity and is not altered by sequence changes); whereas catalytic diversity requires precisely the opposite: a very wide range of three-dimensional shapes (configuration of catalytic sites), which are highly sensitive to variations in the sequence (Moreno and Fernández 1990; Benner 1999).
- 25.
However, RNAs have not been erased by this new world of DNA-proteins, since they still play a crucial role in the complex relations between these two radically different polymers.
- 26.
Here, as explained below, we use in accordance with the definition given in Chap. 1, i.e. as a closed and regulated organisation.
- 27.
Using a linguistic terminology, Pattee (1982) has emphasised the fact that this relation is also subject to organisational closure. According to him, the genetic code should be understood through the idea of “Semantic Closure”. Pattee considers that gene strings are self-interpreting symbols because their action (specific but arbitrary because it is mediated by the recognition of certain functional components) is the synthesis of those components (tRNAs and synthetases) that allow the causal action of the genes themselves. Thus, by contributing to the maintenance of the whole cellular organisation, genes in fact achieve their own interpretation.
- 28.
This is because the particular sequence of its nucleotides is thermodynamically degenerated, in the sense that their order has no notable effect on the distribution of energy throughout the whole molecule. Instead, the alteration of nucleotide sequences in RNAs, and especially modifications in the sequence of amino acids in proteins, usually involve energy changes and therefore three-dimensional changes.
- 29.
In what follows, we will sometimes refer to this kind of specialised templates as « genetic ». This terminological choice is made to bring our usage into line with standard usage in the scientific literature; in turn, it does not imply an interpretation about their nature and role going beyond that which is explicitly provided in these pages.
- 30.
Until radically new forms of organisation (societies, technologies, etc.) emerge, thus transcending the fundamental biological organisation.
- 31.
Since any more complex form would not be preserved unless it were compatible with this organisational structure.
- 32.
With the invention of eukaryotic cell, (thanks, in particular, to the nucleation of DNA) organisms had the possibility for more elaborate regulation and processing of genetic information and, thereby, for a much more complex internal organisation than in prokaryotes. As J. Mattick (2004) has pointed out, in bacteria transcription and translation occur together: RNA is translated into protein almost as fast as it is transcribed from DNA. There is no time for intronic RNA to splice itself out of the protein coding RNA in which it sits, so an intron would, in most cases, disable the gene it inhabits, with harmful consequences for the host bacterium. In eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm, a separation that opens a window of opportunity for the intron RNA to excise itself. Introns can thus be more easily tolerated in eukaryotes. In other words, the decoupling between transcription and translation permitted a much higher level of genetic regulatory control, which, in turn, would be required to increase the organisational complexity and plasticity of the whole cell (Taft et al. 2007).
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Moreno, A., Mossio, M. (2015). Evolution: The Historical Dimension of Autonomy. In: Biological Autonomy. History, Philosophy and Theory of the Life Sciences, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9837-2_5
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