Chemical games and the origin of life from prebiotic RNA

From bacteria to vertebrates, life — as we know it today — relies on complex molecular interactions, the intricacies of which science has not fully untangled. But for all its complexity, life always requires two essential abilities. Organisms need to preserve their genetic information and reproduce.

In our own cells, these tasks are assigned to specialized molecules. DNA, of course, is the memory store. The information it encodes is expressed into proteins via messenger RNAs.Transcription (the synthesis of mRNAs from DNA) and translation (the synthesis of proteins from mRNAs) are catalyzed by polymerases necessary to speed up the chemical reactions.

It is unlikely that life started that way, with such a refined division of labor. A popular theory for the origin of life, known as the RNA world, posits that life emerged from just one type of molecule: RNAs. Because RNA is made up of base-complementary nucleotides, it can be used as a template for its own reproduction, just like DNA. Since the 1980s, we also know that RNA can act as a self-catalyst. These two superpowers – information storage and self-catalysis – make it a good candidate for the title of the first spark of life on earth.

The RNA-world theory has yet to meet with empirical evidence, but laboratory experiments have shown that self-preserving and self-reproducing RNA systems can be created in vitro. Little is known, however, about the dynamics that governed pre- and early life. In a recent paper, Yeates et al. (2016) attempt to shed light on this problem by (1) examining how small sets of different RNA sequences can compete for survival and reproduction in the lab and (2) offering a game-theoretical interpretation of the results.

Cooperation, enzymes, and the origin of life

Enzymes play an essential role in life. Without them, the translation of genetic material into proteins — the building blocks of all phenotypic traits — would be impossible. That fact, however, poses a problem for anyone trying to understand how life appeared in the hot, chaotic, bustling molecular “soup” from which it sparked into existence some 4 billion years ago.

Throw a handful of self-replicating organic molecules into a glass of warm water, then shake it well. In this thoroughly mixed medium, molecules that help other molecules replicate faster –- i.e. enzymes or analogues thereof — do so at their own expense and, by virtue of natural selection, must sooner or later go extinct. But now suppose that little pockets or “vesicles” form inside the glass by some abiotic process, encapsulating the molecules into isolated groups. Suppose further that, once these vesicles reach a certain size, they can split and give birth to “children” vesicles — again, by some purely physical, abiotic process. What you now have is a recipe for group selection potentially favorable to the persistence of catalytic molecules. While less fit individually, catalysts favor the group to which they belong.

This gives rise to a conflict opposing (1) within-group selection against “altruistic” traits and (2) between-group selection for such traits. In other words, enzymes and abiotic vesicles make an evolutionary game theory favourite — a social dilemma.

Did group selection play a role in the evolution of plasmid endosymbiosis?

Bacterial plasmids are nucleotide sequences floating in the cytoplasm of bacteria. These molecules replicate independently from the main chromosomal DNA and are not essential to the survival or replication of their host. Plasmids are thought to be part of the bacterial domain’s mobilome (for overview, see Siefert, 2009), a sort of genetic commonwealth which most, if not all, bacterial cells can pull from, incorporate and express. Plasmids can replicate inside a host and then move to another cell via horizontal genetic transfer (HGT), a term denoting various mechanism of incorporation of exogenous genetic material.

Continuing our exploration of group selection

This Tuesday, I gave the second of two presentations for the EGT Reading group, both focused on the theory of group selection. Though I am currently working outside of academia, it has been a pleasure to pursue my interests in ecology, and our group discussions have proven to be both enjoyable and challenging.

The first presentation [pdf] is a review of a 2011 paper written by Marshall. It argues that when the models underlying inclusive fitness theory (IFT) and group selection are formally identical. However, as I tried to show during the presentation, this formal equivalency only holds for one specific type of group selection – group selection as the partitioning of selection between groups from selection within groups. It no longer holds when we consider the more restrictive definition of group selection as “natural selection on groups” in strict analogy to individual selection (this, incidentally, is the definition of group selection I gave in my last blog post)

Marshall J.A.R. (2011). Group selection and kin selection: formally equivalent approaches, Trends in Ecology & Evolution, 26 (7) 325-332. DOI: 10.1016/j.tree.2011.04.008

The second presentation [pdf] is a review of a paper by Paulsson (2002). That paper presents an interesting case of multi-level (group) selection, where the “individuals” are plasmids – self-replicating gene clusters in the cytoplasm of procaryotes – and the “groups” are the plasmid-hosting cells. It’s a nice illustration of the basic dilemma that drives group selection. Inside a cell, plasmids which replicate faster have an advantage over their cell mates. But cells in which plasmids replicate too fast grow slower. Thus, at the level of individuals selfishness is favored, but at the level of groups altruism is favored. Paulsson’s paper explains the mechanisms of plasmid replication control; sketches up models of intra- and inter-cellular selection gradients; and explains how conflicts between individual- and group-selection are resolved by plasmids. He also considers a third level of selection on lineages, but both Artem and I were confused about what exactly Paulsson meant.

Paulsson, J. (2002). Multileveled selection on plasmid replication. Genetics, 161(4): 1373-1384.

Where did the love come from? Inclusive fitness vs. group selection

Altruism is widespread in the animal world, yet it seems to conflict with the picture of nature “red in tooth and claw” often associated with Evolution. One solution to this apparent paradox is to remember that the unit of selection is never the individual itself but the genes  it carries. Thus, altruism may be explained if the altruist shares genes with the individual it helps in such a way that, while harming itself as an individual, it favors the spread of its genes. This idea of analyzing selection at the level of genes rather than the individual dates back to the 1930s, when Darwin’s theory and Mendelian genetics were first combined to form a unified framework now known as the neo-Darwinian synthesis.

Altruism is a common feature of animal behaviour. In this picture, a chimp mother helping another down a tree. Source: The Selfishness of Giving by Frans de Waal on Huffington Post.