Alien biochemistry

[Avalancheon]

Hi everyone, I'm new to the forum here. I just signed up today, even though I've been reading orions arm for several years. One topic that raised my interest was about the nature of alien biochemistry. Specifically, about organisms that rely on carbon for structure, and water as a solvent. (These are called type 1 life forms in the OA page) Is it inevitable that carbon based life would use DNA and/or RNA to encode genetic information? Are other arrangements possible, or even likely?

A related question: Are there any type 1 biospheres in the OA universe that use something other than DNA? Or that maybe use DNA with different nucleotides, something other than A-G-C-T? I'm trying to learn more about this and am grateful for any answers.

[stevebowers]

I'd guess that about a third of all biospheres in the Terragen Sphere are still in the prebiotic stage, and many of those do not have a dominant form of replicating molecule but are chemical soups of metabolising molecules without genetics. The majority of biospheres do use replicating molecules, however; many will still be in the RNA-world stage, and some of these might be highly sophisticated. Others would use DNA (either dextro- or levo-), but this is not the only possibility by a long chalk.

Below is an image from The Origins of the RNA World (Robertson and Foyce 2012) which gives some alternatives.
(A) RNA; (B) p-RNA; © TNA; (D) GNA; (E) PNA; (F) ANA; (G) diaminotriazine-tagged (left) and dioxo-5-aminopyrimidine-tagged (right) oligodipeptides; and (H) tPNA. (ANA is one I haven't heard of before, and it is formed from a racemic mixture, unlike DNA. So this might support some sort of racemic biochemistry which uses both left-handed and right-handed molecules).

[iancampbell]

I haven't had time to check, but is it not also possible that a DNA analogue could be used - one with the same basic structure but different bases chosen from the many available? There are many purines and pyrimidines, after all.

Or, another possibility: AFAIK the genetic code is completely arbitrary; is it possible that alien life uses DNA with the same bases as ours but a different coding scheme?

And finally, I much doubt that the amino acids we use are the only ones suitable for use in proteins. In fact, there are quite a lot of Earthly proteins that incorporate amino acids there is no code for - they are converted after they go into the protein. The best example is hydroxyproline, used in colossal amounts (it's one of the major components of collagen) but with no DNA code for it at the moment.

[stevebowers]

Is it possible that alien life uses DNA with the same bases as ours but a different coding scheme?

In the Terragen Sphere there are several worlds with biospheres that use DNA (including Seattle, a world described recently by Cray). However it is inevitable that such worlds use a different DNA coding system to Earth, since the chance against the same code occurring on two planets in the Visible Universe is very low indeed.

[Avalancheon]

I'd guess that about a third of all biospheres in the Terragen Sphere are still in the prebiotic stage, and many of those do not have a dominant form of replicating molecule but are chemical soups of metabolising molecules without genetics. The majority of biospheres do use replicating molecules, however; many will still be in the RNA-world stage, and some of these might be highly sophisticated. Others would use DNA (either dextro- or levo-), but this is not the only possibility by a long chalk.

Excellent response. That brings a couple other questions to mind. Is it possible that the 'alien' DNA in these other worlds could have an opposite chirality from terran DNA? Or would right-handed amino acids and left-handed nucleotides make them into something altogether different? And of these different replicating molecules you mentioned (TNA, GNA, PNA, etc), do any of them have advantages compared to DNA? In the prebiotic stage of a biosphere, are they any more likely to evolve and dominate over DNA?

[stevebowers]

I did mention chirality in the post you quoted; there is some evidence that L-DNA and lefthanded biochemistry is favoured naturally, since some of the amino acids found in carbonaceous chondrite meteors have a bias towards left-handedness. But that might be a local phenomenon, possibly originating in our star's formation cloud or in the cluster we originated in. The conditions in other solar systems or clusters might favour right-handedness.

[sandcastles]

Are there examples in OA of a one planet hosting major ecosystems of different biochemistries?  By "major" I just mean something more extensive than things like the chemosynthetic bacteria in acid pools around geysers or oceanic tube worms on our planet. 

Is this likely?  A tidally locked planet has a cold-adapted ecosystem on the cold side, a "normal" carbon based ecosystem in the terminator zone, and a hot-adapted ecosystem on the hot side.  The composition of the atmosphere will be very mixed, I know.  I don't know what the sulfur breathers will do with the methane, or the methane breathers will do with the SO2.

[Worldtree]

Are there examples in OA of a one planet hosting major ecosystems of different biochemistries?  By "major" I just mean something more extensive than things like the chemosynthetic bacteria in acid pools around geysers or oceanic tube worms on our planet. 

Do you mean naturally occurring biochemistries? Because there’s plenty of references to megastructures and orbitals and sections of enclosed habitats on various planets where multiple biochemistries are being cultivated - Neptune’s world shell has many environments, for example. https://www.orionsarm.com/eg-article/4f1828a411675

[stevebowers]

Yes, I expect that numerous worlds in the Terragen Sphere would have multiple biospheres with different biochemistries, or at the very least multiple genetic codings that are not compatible with each other.
Earth probably had several biospheres early in its history. But (if Earth's history is any indicator) then most of these biospheres would die out, and reduce to one single biosphere at some point (or none).

Only a very few garden worlds would have two or more complex, incompatible biospheres, and these would be worth writing about.

[Jagace]

Hi everyone, I'm new to the forum here. I just signed up today, even though I've been reading orions arm for several years. One topic that raised my interest was about the nature of alien biochemistry. Specifically, about organisms that rely on carbon for structure, and water as a solvent. (These are called type 1 life forms in the OA page) Is it inevitable that carbon based life would use DNA and/or RNA to encode genetic information? Are other arrangements possible, or even likely?

A related question: Are there any type 1 biospheres in the OA universe that use something other than DNA? Or that maybe use DNA with different nucleotides, something other than A-G-C-T? I'm trying to learn more about this and am grateful for any answers.

Hi, biochemist and carbon chauvinist here. It's certainly possible for DNA life to use other nitrogenous bases. In the field of synthetic biology, "hachimojo DNA" has been created, with four additional bases. In our DNA we have the A=T and C≡G pairs, but hachimojo DNA can also have P≡Z and B≡S pairs. Check its Wikipedia article for more sources and the structure of these molecules. In sum, the hachimojo system works for both DNA and RNA, which can be transcribed (but not translated, as the researches didn't create a suitable genetic code) and even showed ribozyme activity.

However, I'd bet that some nitrogenous bases are very common even in extraterrestrial life, due to the easiness of their synthesis. For example, take adenine. Its chemical formula is C₅H₅N₅, which is a pentamer of hydrogen cyanide (HCN). Syntheses mimicking primitive Earth-like conditions have been known since the 1960s.

I think that life isn't necessarily made of the best molecules possible, but the ones that were most available during the prebiotic Earth. 

In the hachimojo example, consider how base Z has a nitro group, a functional group that is extremely rare in living organisms (in fact, I don't recall seeing it in any biological compound during my undergraduate years). Even if this base provided a superior form of biochemistry, it simply wouldn't have come around because its natural synthesis is very unlikely.

Anyhow, OA does have an example of an (arguably) naturally occurring expanded nucleic acid life, on Baryos:

Life on Baryos is not very exotic, being based on left-handed amino acids, a nucleic acid using six nucleotides, and with starches doing many functions performed by proteins in terrestrial life.

Take also a look to the abiogenesis article, to know more about the "lore" of abiogenesis in OA. It does mention explicitly which nucleic acids are known to have been found on primitive worlds:

Examples of this Nucleic Acid world stage are widespread, and molecules such as RNA, PNA, TNA and even DNA are found in simple cells known as protobionts, often associated with the previously mentioned PAH compounds.

Strangely though, I couldn't find any mentions of what OA's most popular xenosophonts (like to'ul'hs and muuh) use as their genetic material. The to'ul'h however could be DNA-based, as we already know of examples of hyperthermophile life on Earth.