Question 9: Prospects for the Construction of Artificial Cells or Protocells

The construction of artificial cells or protocells that are a simplified version of contemporary cells will have implications for both the understanding of the origins of cellular Life and the design of “cell-like” chemical factories. In this short communication, we discuss the progress and remaining issues related to the construction of protocells from metabolic products. We further outline the de novo design of a simple chemical system that mimics the functional properties of a living cell without being composed of molecules of biological origin, thereby addressing issues related to Life’s origins. Presented at: International School of Complexity—4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

The origins and key innovations of vertebrates and arthropods

The Lower Cambrian Maotianshan Shale near Kunming (Southern China) not only retains beautifully preserved and diverse organisms but also documents a missing evolutionary history between living vertebrates and their amphioxus-like ancestor. Presented here are the key novelties both for the evolutionary origins of the chordates and for the evolutionary transition from amphioxus-like ancestor toward the vertebrates. The adaptation for a burrowing life style is considered a key adaptive pressure for generating novel chordate-only anatomical characters including the first axial skeleton, e.g., notochord and myotomes. The transition from amphioxus-like ancestor toward the vertebrates was presumably triggered by the way toward more active life style, resulted in the origination of numerous novel structures including neural crests, a more complex head with upper and lower lips, an active gilled pharyngeal system, a large brain, image-forming paired eyes, and a bony axial skeleton (vertebrae). The diverse limb-bearing organisms from the Lower Cambrian Maotianshan Shale arthropods representing different evolutionary stages shed light on the mysterious field of the evolutionary origins of the arthropods and reveal a grand scenario of how the arthropods paved their way through step-wise evolution from worm-like ancestor toward living crown-lineage arthropods.     

The Neolithic of the southern Levant

The Neolithic period of the southern Levant was an era of tremendous change. Over the course of the Neolithic, the gradual transition from foraging to agriculture involved not merely economic innovations, but also profound shifts in population size, social organization, and technology. This represents possibly the earliest, and certainly one of the earliest, instances of the transition to agriculture. The advent of farming altered human demography, health, and diversity; it shaped the spread of the world's dominant cultures, genes, and languages. 1 , 2 It recast humans' relationship with the natural world, increasing modification of the environment. It both enabled and required the development of new social structures as humans learned how to live in increasingly large and densely packed groups. These transformations were not easily achieved. This paper traces the development of the southern Levantine Neolithic through two thousand years of socioeconomic elaboration and expansion; a major social recalibration in the middle Neolithic; and a final millennium‐and‐a‐half of smaller‐scale and materially simpler adaptations.     

Solubility, adsorption, and the thermodynamics of the cutoff effect

For many years, the expression "cutoff effect of anesthesia," has been used to denote the failure of the higher alcohols or paraffins to produce anesthesia. As such, it is used to assess the plausibility of specific models, proposed for anesthesia. However, the uses were shown, in many respects, to be problematic. This article augments the notion of the cutoff to fit for all cases in which only some of the molecules in a homologous series are anesthetics. We find that the location of the cutoff points is affected by three free energy quantities: that of the adsorption of the agent to the anesthetic "site" (f(sl,site)), that of the perturbation of the site (f(ll,site)), and that of the evaporation of the agent from its pure condensed phase (Deltamu degrees (evaporation)). This outcome indicates that the cutoff cannot be attributed to a single parameter. In addition, the analyses that attribute the cutoff to the failure of compounds to obey the much-used Meyer-Overton correlation will have to be amended. This article shows that cutoff results can be used to elucidate the structure of a site.     

Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life

Protein evolution is imprinted in both the sequence and the structure of evolutionary building blocks known as protein domains. These domains share a common ancestry and can be unified into a comparatively small set of folding architectures, the protein folds. We have traced the distribution of protein folds between and within proteomes belonging to Eukarya, Archaea, and Bacteria along the branches of a universal phylogeny of protein architecture. This tree was reconstructed from global fold-usage statistics derived from a structural census of proteomes. We found that folds shared by the three organismal domains were placed almost exclusively at the base of the rooted tree and that there were marked heterogeneities in fold distribution and clear evolutionary patterns related to protein architecture and organismal diversification. These include a relative timing for the emergence of prokaryotes, congruent episodes of architectural loss and diversification in Archaea and Bacteria, and a late and quite massive rise of architectural novelties in Eukarya perhaps linked to multicellularity.Reviewing Editor : Dr. David Pollock     

Phenotypic diversity and chaos in a minimal cell model

Gánti's chemoton model (Gánti, T., 2002. On the early evolution of biological periodicity. Cell. Biol. Int. 26, 729) is considered as an iconic example of a minimal protocell including three key subsystems: membrane, metabolism and information. The three subsystems are connected through stoichiometrical coupling which ensures the existence of a replication cycle for the chemoton. Our detailed exploration of a version of this model indicates that it displays a wide range of complex dynamics, from regularity to chaos. Here, we report the presence of a very rich set of dynamical patterns potentially displayed by a protocell as described by this implementation of a chemoton-like model. The implications for early cellular evolution and synthesis of artificial cells are discussed.     

On the Origins of a Crowded Cytoplasm

Contemporary cells show a highly crowded macromolecular content, the processes which originated this state being largely unknown. We propose that a driving force leading to the crowded cellular state could be the increase in growth rate produced by an enhanced cytoplasmic protein concentration. Briefly, in a diluted scenario, an increase in protein concentration has two opposing effects on growth rate. The favorable effect is the increase in the activity per unit volume of the component proteins and the disadvantageous effect is the concomitant increase in the protein mass per unit volume which has to be produced. In this work we show that the first effect is quantitatively more important, resulting in an overall increase in growth rate. This result was obtained with a model of E. coli and using nonmechanistic physiological arguments. The proposed driving force operates even at low protein concentrations, where the nonspecific interactions of macromolecular crowding are not significant, and could be as ancient as the first protocells. Experimental measurement of this cytoplasmic protein concentration effect in present organisms is hindered by the prevailing nonspecific interactions, product of long-term evolution. However, chemical/biochemical systems, built up to mimic properties of living cells, could be an adequate tool to test this effect. [Reviewing Editor: Dr. Antony Dean]     

Hanuman Langur: Monkey of India

An apparently new type of dental wear pattern, lingual surface attrition of the maxillary anterior teeth (LSAMAT), has been found in 85% of 46 adult crania from a 3000–4200 BP Archaic site called Corondó near the Atlantic Ocean coast of Brazil. LSAMAT is associated with a high caries rate (60% of 77 adults; 11% of 1,219 permanent teeth) in what on archeologica grounds alone would be considered a mainly meat-eating population. It is suggested that both LSAMAT and caries resulted from eating some starchy plant like manioc.     

Evolution in biological and nonbiological systems under different mechanisms of generation and inheritance

The majority of definitions of life and evolution include the notion that part of an organism has to be copied to its offspring and that this includes some form of coded information. This article presents the thesis that this conception is too restrictive and that evolution can occur in systems in which there is no copy of information between generations. For that purpose, this article introduces a new set of concepts and a theoretical framework that is designed to be equally applicable to the study of the evolution of biological and nonbiological systems. In contrast to some theoretical approaches in evolution, like neo-Darwinism, the approach presented here is not focused on the transmission and change of hereditary information that can be copied (like in the case of DNA). Instead, multiple mechanisms by which a system can generate offspring (with and without copying) and by which information in it affects the structure and evolution of its offspring are considered. The first part of this article describes in detail these new concepts. The second part of this article discusses how these concepts are directly applicable to the diversity of systems that can evolve. The third part introduces hypotheses concerning (1) how different mechanisms of generation and inheritance can arise from each other during evolution, and (2) how the existence of several inheritance mechanisms in an organism can affect its evolution.