I cannot make further progress on my sci-fi novel until I have an idea of alternate biochemistries likely to be found on other worlds. It will be an epic story, so I’ll want several alternate biochemistries. (What alternate biochemistries are proposed in other sci-fi novels?)
It would help if I first understand our own biochemistry better. The key complex molecules for Earth’s life are nucleic acids and proteins, based respectively on {CO(PO[sub]2[/sub])OCC}[sup]N[/sup] and {CNC}[sup]N[/sup] chains. Earth’s complex life uses two different types of nucleic acid (DNA for replication, RNA for protein synthesis); is this to be expected? Maybe some exo-life might even use three different types? Or perhaps, as is believed about Earth’s early life, just a single type of complex molecule (e.g. replicating RNA without proteins) could evolve into complex life.
What is the “purpose” of the phosphate in nucleic acid? Could sulfate be substituted? For complex enzymes, are there good alternatives to proteins (amino acid chains)? Sugar and phosphate are key molecules in metabolism on Earth; are there good alternatives?
Earth’s life depends on a bath of water. Water has several very useful properties, almost spectacularly so. I think an acid (sulfuric?) diluted with water would be one alternative solvent. Is liquid ammonia (or methane) a plausible alternative, or should I just assume water will always be the key solvent?
Instead of chains based primarily on carbon, the only likely alternative seems to be silicone {SiO}[sup]N[/sup], though even here any side-chains would still probably be based on the elements C,N,O,H. (Silicone bonds are much more stable than the bonds in protein, but I think this won’t cause trouble, at least if the water solvent is acidic enough.)
At least one of the life forms in my epic will be completely extinct but will have left behind an “artificial life.” For the neural circuits in that artifical life, I might use gallium arsenide crystals.
As a biologist and sci-fi fan (but not a writer…) have some unsolicited pre-coffee writing advice!
Don’t dwell too much on the details of alien biology in your story. In my experience, stories that do are often jaw-droppingly stupid, in a “not even wrong” kind of way. Nearly every mention of biology in Star Trek, for example, is egregiously wrong. There are a handful of examples where the details are plausible and intriguing, but this makes for a tedious story – here I’m thinking of Peter Watts’ novels.
The best sci-fi treatments of alien biology, in my opinion, don’t focus on the details. I’ve been most impressed by the biology of novels like The Expanse series, and The Southern Reach trilogy. From what I recall, the scientists in those stories speak mostly in generalities and analogies, which is usually how scientists have to talk to non-scientists anyways. The specifics are limited to instances that are directly relevant to the main characters: “can I eat that”, “will it infect me”.
That isn’t to say you shouldn’t try to work out the details, just use them more for world-building and background.
(For life as we do know it, you couldn’t do much better than the books of Nick Lane, especially including The Vital Question and Life Ascending: The Ten Great Inventions of Evolution.)
I agree - I mean, it’s nice sometimes to be thrown some incomplete fragments of description and exposition in passing, like, say, if a character says something like “Of course ‘genome’ isn’t even a relevant term in the context of flurpian biology, because although there is heredity and mutation, the mechanisms and processes aren’t anything like they are for Terran life - there’s no DNA; there are no chromosomes; there are no cell nuclei, heck, we’re not even really comfortable that the term ‘cell’ adequately fits the units these organisms are made out of…”
If a character says that, the problem with the story is not the science.
If you really have a need to cover it, the sentence would be “Of course ‘genome’ isn’t strictly accurate, but let’s use it for now.” But the question you need to ask is “why is this important to the characters?”
In science fiction, you only have to talk about what’s important to the story, not the background. If people are nitpicking the science, the story has failed on other levels.
If you could find a summary of Cairns-Smith’s work that might be quite thought-provoking. He was interested in the idea that inorganic clay minerals could have been a primitive genetic system that preceded, and birthed, our biological one. Some concepts of information transfer and evolution can be identified in how crystals grow, and inorganic catalysis of biological processes is a fact of life.
His ideas in this area were very speculative, but are well regarded for their originality and might be useful from the POV you’re interested in.
Why we have the molecules we have for these fundamental metabolites is a pretty deep question, that makes thinking of credible alternatives quite difficult. The amide linkage of proteins, for example, is easily appreciated as being pretty robust and stable - so we don’t dissolve in the rain. But it is also quite stiff, it the amide just the right amount of rigidity for proteins to form ternary structure - without structure there is no function. If you were to make a biopolymer with ester units, say, displaying identical amino acid side-chains, it would be too floppy to function as a protein [amongst other issues].
Peptide DNA exists (PNA) - an amide backbone displaying nucleobase residues, which will bind to a complimentary strand and form a duplex. The lack of a charged phosphate group in comparison to DNA means it actually binds more tightly - too tightly for hypothetical biological roles [plus it is considerably less water soluble], but it has a variety of uses as a tool in molecular biology.
I bet there’s been some SF stories on enantiomeric life - mirror image proteins, carbohydrates, DNA, fats. Obv you don’t want to retread old ground but maybe something there to spark a few ideas.
One option is to focus less on the key biomolecules and instead think about the fuel and exhaust products. Plants use light to convert CO2 and H2O into carbohydrates and oxygen. Plants and animals convert carbohydrates and oxygen into energy. But there are plenty of processes even on our own planet that don’t involve the formation of consumption of elemental oxygen, which is a pretty reactive gas that may very well be completely incompatible with your aliens.
The only sensible things we can say about any xenobiological system is that it is very likely to be based on a CHONPS chemistry (given the universal abundance of those elements), that it will form something akin to proteins to provide functional mechanisms, and that complex life will almost certainly have a cellular-like organization. (A further unstated rule is that it will operate on thermodynamic principles and seek to work by moderating energy flows, but that should be regarded as definitional for life.)
it is very tempting to believe that life must evolve in some kind of solvent–water is particularly convenient because of its weakly polar nature which can be enhanced by salts, but a weak acid or liquid hydrocarbon is certainly feasible–but you might see exotic chemistries in a highly ionizing environment that wouldn’t be possible in a liquid medium, or some kind of gaseous convection-based medium without solid structures as well. We might be hard pressed to recognize these as “life” due to both the size and time scale that they might operate on, but it is remotely plausible.
The use of silicon chain polymers in the place of carbon-based backbones has been long suggested but there are a number of reasons to find this dubious. I wouldn’t dismiss it out of hand, but carbon (and carbon-nitrogen bond in particular) seem to be ideal as be basis structure for such a vast array of complex chemical formations and the elements are so universally available that it is hard to imagine another competing chemistry system that would evolve into a self-replicating form naturally. If you are going to consider silicon then you might was well consider germanium and arsenic, or antimony, tellurium, and iodine (which would admittedly make for some pretty wild xenobiochemistry).
As lazybratsche suggests, I wouldn’t focus too much on the details, as you are inevitably going to throw something in that a reader knowledgable in biochemistry will immediately determine to be wrong. It is better to throw in a couple of hints about the differences and leave it to the reader, if they are so inclined, to fill in the details unless it is somehow key to the story, in which case you should be confidence in your facts, even if (or especially) if they are factually incorrect.
One other element to play with is the triplet coding of t-RNA (transfer). Essentially all* terran life uses the same code so that a sequence of three nucleotides codes for the same amino acid using the same genetic code regardless of which organism.
You could explore ideas like what a alien virus or bacteria might turn into if a different genetic code was used. Or this could be a means of how an extinct species could be revived by figuring out what genetic code it evolved with.
Thank you for all the excellent suggestions! There’s a lot of information here.
I did find an on-line (pdf) copy of Cairns-Smith’s Seven Clues to the Origin of Life. I was already behind on my reading and now I’ve got my work cut out for me!
That is a fascinating article. I’ve wondered if the genetic code was arbitrary or instead based on some chemical fit between codon and amino acid. It sounds like the answer is “Maybe.”
I was intrigued by “H. Murakami and M. Sisido extended some codons to have four and five bases.” The Wiki article had no cite for this but Google showed one. However I found it baffling and didn’t even try to wade through the Abstract.
~ ~ ~ ~ ~ ~ ~
The novel won’t go into a lot of detail, but I want the very basics to be correct. I think the silicone-based life will arise on planets with very acidic oceans. Life-forms based on methane or ammonia solvents will have extremely slow metabolisms — will they still be able to develop complex life?
The powerful inter-galactic civilization conducting a survey will find many planets with life, but very few that developed high technology. I think most of the advanced life will rely on protein or something similar, but some may be silicone-based.
And why are nucleic acids based on phosphate? Is there a plausible alternative?
The phosphate group includes 4 oxygens with substantial negative charge. When two phosphate groups are joined, the resulting phosphoanhydride bond has high energy – think of it as the energy that’s required to push two negatively charge groups close together, overcoming electrostatic repulsion, close enough for the bond to form. Conversely, if the bond is broken, the electrostatic repulsion pushes the two phosphate groups apart, releasing energy.
High energy phosphate bonds are the energy currency of all life, in the form of ATP, Adenosine Triphosphate. The energy in ATP phosphate-phosphate bonds is used to drive most of the reactions of cellular metabolism. The human body contains about 8oz of ATP, but we recycle our body weight in ATP daily as it is constantly used and recharged.
When DNA is synthesized, the building blocks are very similar to ATP: dATP, dCTP, dGTP, dTTP. The d stands for deoxy (a property of the sugar moiety), the leading A/C/G/T are the 4 bases, and -TP stands for triphosphate. In other words, to form the DNA polymer, you start with “charged” nucleotides containing these high energy phosphate-phosphate bonds. This energy drives the polymerization reaction forward, since the DNA polymer contains lower energy phosphodiester bonds, in which just a single phosphate group joining the sugar moieties along the backbone. The phosphate group in the backbone is hydrophilic, while the bases are hydrophobic. This puts DNA in a stable configuration with the backbone exposed to solvent on the outside, and the bases hidden from solvent in the interior. This is where the bases need to be in order to hydrogen bond with the opposite DNA strand, giving each strand the ability to template the synthesis of the other.
So, in summary: high energy phosphoanhydride (phosphate-phosphate) bonds are the energy currency of the cell, that’s the principal reason phosphate groups are around in the first place; DNA synthesis is one metabolic reaction that’s driven by breaking high energy phosphate-phosphate bonds; the single phosphate that’s left can form a stable phosphodiester bond to make the backbone of the DNA; and phosphate is hydrophilic, something that you want in the backbone.
Thank you, Riemann; that was very helpful. Especially the notion that the hydrophilic phosphates make it easier for DNA strands to bond.
Does sulfate have similar properties? I note that phosphorus is, very roughly, about three times more common than sulfur in both Earth’s crust and human body.
Would it be out of line if one planet’s life used “replicating molecules very similar to RNA but with sulfate playing the role of phosphate”?
