The RNA hypothesis is very popular but doesn’t explain how fragile RNA can survive in hostile environments.

Dr. Joyce has been studying the possible beginning of history by developing RNA molecules with the capacity for replication. RNA, a close cousin of DNA, almost certainly preceded it as the genetic molecule of living cells. Besides carrying information, RNA can also act as an enzyme to promote chemical reactions. Dr. Joyce has developed 2 RNA molecules that can promote each other’s synthesis from the 4 kinds of RNA nucleotides. “We finally have a molecule that’s immortal”

2016-02-21: Talk of RNA-like

Perhaps before biology arose, there was a preliminary stage of proto-life, in which chemical processes alone created a smorgasbord of RNAs or RNA-like molecules. “I think there were a lot of steps before you get to a self-replicating self-sustaining system”. In this scenario, a variety of RNA-like molecules could form spontaneously, helping the chemical pool to simultaneously invent many of the parts needed for life to emerge. Proto-life forms experimented with primitive molecular machinery, sharing their parts. The entire system worked like a giant community swap meet. Only once this system was established could a self-replicating RNA emerge.

2019-06-30: Viroids, survivors from the RNA World?

Because RNA can be a carrier of genetic information and a biocatalyst, there is a consensus that it emerged before DNA and proteins, which eventually assumed these roles and relegated RNA to intermediate functions. If such a scenario–the so-called RNA world–existed, we might hope to find its relics in our present world. The properties of viroids that make them candidates for being survivors of the RNA world include those expected for primitive RNA replicons: (a) small size imposed by error-prone replication, (b) high G + C content to increase replication fidelity, (c) circular structure for assuring complete replication without genomic tags, (d) structural periodicity for modular assembly into enlarged genomes, (e) lack of protein-coding ability consistent with a ribosome-free habitat, and (f) replication mediated in some by ribozymes, the fingerprint of the RNA world. With the advent of DNA and proteins, those protoviroids lost some abilities and became the plant parasites we now know.

2022-05-06: RNA “species”

Over 100s of hours of replication, 1 type of RNA evolved into 5 different molecular “species” or lineages of hosts and parasites that coexisted in harmony and cooperated to survive, like the beginning of a “molecular version of an ecosystem”. Their experiment, which confirmed previous theoretical findings, showed that molecules with the means to replicate could spontaneously develop complexity through Darwinian evolution. Some of these results confirmed the predictions of earlier experimental studies of how complexity can arise in viruses, bacteria and eukaryotes, as well as some theoretical work.
“Without parasites, this level of diversification is probably not possible”. Evolutionary pressures that parasites and their hosts place on each other lead both sides to split into new lineages.

2024-02-01: Obelisks

A new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. These “obelisks” have genomes seemingly composed of loops of RNA and sequences belonging to them have been found around the world. The Stanford search yielded 30k predicted RNA circles, each consisting of ~1000 bases and likely representing a distinct obelisk. They were unlikely to be bona fide viruses because RNA viruses typically have many more bases. But some of the obelisk sequences encoded proteins involved in RNA replication, making them more complex than standard viroids. Like viroids, however, obelisks don’t seem to encode proteins that make up a shell. Because obelisks contain genes that are unlike any discovered so far in other organisms, they “comprise a class of diverse RNAs that have colonized, and gone unnoticed in, human, and global microbiomes”

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