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Humans are terraforming what they believed to be a barren planet when they encounter a new species of bacteria. This species is exobacteria (bacteria of extraterrestrial origin), but the human scientists can't immediately tell. The species should be sufficiently biologically similar to be able to pass for terrestrial under a microscope and to biologically interact with the terrestrial ecosystem the humans are building. The exobacteria have some surface proteins that are new but identifiable as proteins. The exobacteria are nitrogen-fixing bacteria able to fill a role in the terrestrial nitrogen cycle (or at least fill this well enough to cause trouble).

But the exobacteria DNA can't be sequenced using future-standard DNA sequencing technology because they don't actually have DNA! What do the exobacteria have instead DNA that sill allows them to synthesize proteins?

As an alternative formation of the question, which if the following is most plausible?

  • The exobacteria has a pseudo-DNA with isomers for all four base pairs (A, T, C, and G), such as uracil instead of thymine. I'd find it acceptable that the a future DNA sequencer is sufficiently specialized at reading terrestrial DNA that it ignores isomers.
  • The exobacteria assembles the standard amino acids into chains using some mechanism other than DNA (or at least not strictly isomorphic to terrestrial DNA).
  • The exobacteria assembles proteins using something other than terrestrial amino acids.
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  • $\begingroup$ Hi Zags, welcome to Worldbuilding! Your questions sounds like "a story set in the world". Is the main problem here that an out-of-the-box DNA sequencer used by your characters can't process alien DNA? $\endgroup$
    – Alexander
    Mar 24, 2021 at 23:48
  • $\begingroup$ @Alexander The problem is that they don't technically have DNA. If they have something similar (see isomers), it's at least molecularity different enough to not scan as DNA. I'm wondering the bacteria could have that would serve a similar role in protein synthesis. $\endgroup$
    – Zags
    Mar 25, 2021 at 0:10
  • $\begingroup$ It seems highly unlikely that bacteria from an alien biogenesis have by random mutation and natural selection have come up with anything remotely like what we see on Earth. why pentose sugars? why the bases A,T,C and G and not some other pyrimidines and purines or something else entirely? Why 4 types and not 2 or 8? Why the amino acids we see and not some other amino acids or a different class of compound entirely. Chances are the alien biochemistry would be utterly incompatible with Earth based life. $\endgroup$
    – Slarty
    Mar 25, 2021 at 0:16
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    $\begingroup$ Excellent edit. Close vote withdrawn, nice question. $\endgroup$ Mar 25, 2021 at 0:26
  • $\begingroup$ Your organism has evolved in close association with terrestrial organisms, or else the odds of being similar are exceedingly low. Willk suggested a panspermian event, and perhaps this organism evolved independently, then was exposed to terrestrial-like life and evolved closely to use the same sugars and amino acids because that is what was abundant in it's environment. But for this to work, you'd need to buy into a panspermian event. I didn't give this as an answer because I didn't think panspermia met your requirements. $\endgroup$
    – DWKraus
    Mar 25, 2021 at 0:47

2 Answers 2

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Xenonucleic acids

xenonculeic acids

Xenonucleic acids are artificial structures that can substitute for the natural nucleic acids.

The molecules that piece together to form the six xeno nucleic acids are almost identical to those of DNA and RNA, with one exception: in XNA nucleotides, the deoxyribose and ribose sugar groups of DNA and RNA have been replaced with other chemical structures. These substitutions make XNAs functionally and structurally analogous to DNA and RNA despite being unnatural and artificial... While DNA is incredibly efficient in its ability to store genetic information and lend complex biological diversity, its four-letter genetic alphabet is relatively limited. Using a genetic code of six XNAs rather than the four naturally occurring DNA nucleotide bases yields endless opportunities for genetic modification and expansion of chemical functionality.[9]

Your alien bacteria uses DNA for its genome but sequencing attempts fail because the tech hangs up on the xenonucleotides. I envision your alien organism as fundamentally similar to earth life - maybe because of some sort of panspermia event. Maybe it is life descended from the RNA world. Maybe its unusual nucleotides are borrowed from the modified nucleotides of transfer RNA.

Or maybe it is an engineered creature and the xenonucleotides are synthetic. Your people find it first because it is the most common engineered creature. There are others.

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    $\begingroup$ I must confess, Willk, I have been following your work on worldbuilding for a while, and was hoping I'd get an answer from you on this question. $\endgroup$
    – Zags
    Mar 25, 2021 at 0:19
  • $\begingroup$ Zags you are too kind. Especially to glorify my rambling as "work!" $\endgroup$
    – Willk
    Mar 25, 2021 at 0:57
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XNAs (done)

Willk's answer is a good one, though for some reason he left out PNA, the very first of the alternate backbones.

Alternate nucleotides

There are other nitrogenous bases that appear in our biochemistry as nucleotides (notably flavin and nicotinic acid/nicotinamide)- I have a question up on biology.SE about them.

Panspermia

Recent work showed that the zodiacal light is dust from Mars that stretches all the way to Earth, in such quantity that the Juno probe detected it serendipitously and people can see it with the naked eye! Also note the prevalence of interstellar objects, which may actually be the majority of objects in the region of the Oort cloud, including interstellar comets and asteroids. (See Paul Gilster's recent article at Centauri Dreams

Convergence

The most impossible idea is the one that instinctively appeals to me. What if life, originating somewhere else, simply follows a very similar path? That may seem implausible, but let's go with the model that the formose reaction on a hydroxyapatite substrate creates phosphate-bound sugars, including actual ribose. (ref) Basically, formaldehyde from a geologic source reacts on an inorganic calcium phosphate mineral, perhaps doped with a few interesting metal ions. This has the potential to form a phosphoribose or related sugar backbone, with which amines could react at the aldehyde position. That reaction has a three-carbon intermediate, and phospholipids adhere to hydroxyapatite to this day, causing struvites and clogged arteries. Last but not least, the calcium might chelate dicarboxylic acids, as are seen at alternate ends of the Krebs cycle (oxobutanedioic acid and 2-oxopentanedioic acid). Add NH3 to make glutamate and aspartate, then glutamine and asparagine - that's four amino acids right there. A huge part of our biochemistry might have been established right on the rock, with a patch of hydrophobic products on the way to becoming phospholipids to act as a chemical "filter feeding mechanism". It is conceivable the same could have happened elsewhere in the universe, leading to life forms compatible enough that, with vigorous defenses against toxic compounds, they might be able to view us as prey.

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  • $\begingroup$ I like "right on the rock", The earliest days. Our clay ancestors. $\endgroup$
    – Willk
    Mar 25, 2021 at 0:59
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    $\begingroup$ Clay is popular, but I'm sticking with calcium phosphate minerals only. Life is just a way for bones to get up and walk around the planet. :) $\endgroup$ Mar 25, 2021 at 1:01
  • $\begingroup$ +1, but the convergence part was just showing off ;) $\endgroup$
    – DWKraus
    Mar 25, 2021 at 1:05
  • $\begingroup$ Convergence has always seemed quite likely to me. Life on earth has evolved primarily from a selection and construction of the top five or so elements in the universe. The basic conditions under which life evolved on earth are very commonplace, so I'd expect to see most life evolve carbon-based with more or less the same chemistry. Likely some variation on Amino Acids. We might well even find Exo-DNA. It probably wouldn't be compatible meaningfully with our own, but I'd expect to find most life is fairly comparable chemically speaking. $\endgroup$
    – Ruadhan
    Mar 25, 2021 at 14:44

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