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DISCLAIMER: I am an (intensely interested) layman, not a scientist. Please take my summation of the following concepts accordingly.

I'm currently trying to worldbuild a plausible alien species down to the level of basic biochemistry, and at the moment I'm looking for alternative systems to RNA/DNA that can pass on genetic information. I'm not talking about stuff that essentially just uses the central principle and structure of DNA with some of the specifics changed, like XNAs which just use a different sugar backbone, or Hachimoji DNA which just adds on extra base pairs, I'm talking about plausible hypothesised systems that are radically different to what we use now.

One of the more out-there proposals I've come across is Graham Cairns-Smith's clay hypothesis, which posits that clay crystals were the first genetic material. The idea here is that crystal growth is a form of self-replication that "reproduces" its arrangement, and can even transmit defects. The pattern is then "passed along" when the crystal breaks (scission) and continues to grow independently from the original crystal. Eventually, a "genetic takeover" of sorts happens, where clay crystals that trap certain forms of molecules to their surface improve their replication and catalyse the formation of increasingly complex proto-organic molecules that eventually take over the original genetic substrate as the new genetic material.

Schulman, Yurke and Winfree in their paper "Robust self-replication of combinatorial information via crystal growth and scission" use the same principles to create a set of DNA "tiles" that replicate its sequence of tiles through crystal growth. Each tile has "sticky ends" that hybridise with each other, and under appropriate growth conditions, complementary sticky ends hybridise, while non-complementary sticky ends are unlikely to interact. The interaction of these sticky ends allows for accurate sequence replication during growth, and once crystal growth has propagated the sequence, these additional layers are then "cleaved" off through mechanical scission.

Another early Earth candidate for genetic material, advanced by C. P. J. Maury, is amyloid structures - a "β-sheet peptide-based prion-like amyloid system". It's posited that under the harsh prebiotic conditions of early Earth, beta-sheets would have been a plausible candidate for genetic material, since it is resistant to both UV and ionising radiation, and to high temperatures. Amyloids can catalyse their own replication, and in similar fashion to prions, can transfer conformational information, the changed three-dimensional architecture, to daughter molecules. (Would this essentially make early evolution Lamarckian?) In a paper, Maury, Liljeström and Zhao demonstrate the plausibility of the amyloid world hypothesis by creating a peptide called "EGGSVVAAD" that spontaneously forms amyloid fibrils.

However, there are only a handful of novel ideas surrounding this I am aware of, and I'm not entirely sure if and how any of these systems of replication could achieve a significant level of biological complexity (save for something like a "genetic takeover" that effectively replaces the original system), because for complexity the information needs to not only self-replicate but also be interpreted as instructions for building things. I'm not aware of any paper for now that confidently advances a novel system explaining how an alternative replicator mechanism can be translated in this manner. The way DNA/RNA is translated is a fairly convoluted multi-step process and building such a system for any hypothetical replicator is probably very difficult. Most of the papers I come across are at the very basic level of "how can a sequence of information robustly self-reproduce and transmit its characteristics in a way that selection can operate on it", that additional layer of complexity surrounding translation is unfortunately not touched on (either because it's not part of their intention to create a general purpose replicator, or because they can't propose one).

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    $\begingroup$ Excellently researched question. Interesting topic to which my best answer is: - I've no clue. Watching. $\endgroup$ Commented Aug 8, 2023 at 21:25
  • $\begingroup$ A nitpicking note: 'Maury, Mikko and Fang' are actually Maury, Liljeström and Zhao (or Carl, Mikko and Fang if you're buddies). $\endgroup$
    – Cloudberry
    Commented Aug 9, 2023 at 18:57
  • $\begingroup$ Argh, stupid mistake on my part @Cloudberry. Thanks for pointing it out, have edited the post. $\endgroup$ Commented Aug 9, 2023 at 19:17
  • $\begingroup$ Hi the-protean, this question has an infinite number of equally valid answers. On WB.SE, we discourage "brain storming" questions like this. Asking a question with multiple possible answers is fine, but you need to be very clear about what qualities a best possible answer should have. $\endgroup$
    – Nosajimiki
    Commented Aug 9, 2023 at 21:32
  • $\begingroup$ Just bear in mind that at this point there is no system of replication which could achieve a significant level of biological complexity beyond theoretical mechanisms such as what you have found. Before answering “other” such systems, we should begin with an idea of the one which could explain ourselves. That doesn’t exist. So all of your proposals are on an equally theoretical footing. Choose one which you can best articulate, and build the world. $\endgroup$
    – Vogon Poet
    Commented Aug 10, 2023 at 5:14

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“I'm currently trying to worldbuild a plausible alien species down to the level of basic biochemistry”

The scope for novel molecules in chemistry is vast beyond imagination as there are more possible chemical compounds than there are atoms in the universe. From this perspective humanity knows virtually nothing of the possibilities of what might be achieved chemically. Even restricting the search to “just” existing terrestrial biochemistry doesn’t help much. Have a look at this link and scroll around using the arrow keys on the bottom right

http://biochemical-pathways.com/#/map/1

This is just a fraction of the real chemistry of life on Earth. The task that you have set yourself is daunting.

Are there any alternative systems that would allow for the development of emergent complexity? As far as I am aware nobody knows for sure, but given the above I strongly suspect that there are many that could arise given a different arrangement of starting materials and conditions.

You might find this book by Nick Lane to be of interest: https://en.wikipedia.org/wiki/The_Vital_Question

Alkaline thermal vents produce exactly the conditions required for the origin of life. A high flux of carbon and energy directed over inorganic catalysts. The vent fluids also contain methane, ammonia hydrogen and sulphide and these vents don’t have a central vent they are more like sponges that can concentrate organic materials via thermophoresis. (Note the alkaline vents are distinct from the so called “black smokers”).

He also has an interesting take on the emergence of eukaryotic cells suggesting that their emergence was a highly unlikely fluke event. If true we might expect any other life to be limited to single celled organisms on energy grounds.

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