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I'm about halfway through a novel about a very advanced alien civilization that is systematically wiping out other species using engineered viruses.

I am hoping to have the protagonists test samples in order to prove that the viruses have been designed, and then confront the designers, but that's where I need some input. Other than the fact that these are novel diseases that are unique to each species, would it even be possible to identify signs of unknown modifications in an organism - specifically a virus? My hunch is that there would be no way to tell simply by analyzing the genome, but I could be wrong. Apparently our current technology does not allow for this level of identification, but a sufficiently advanced culture might be able to do it. Currently, I am leaning towards explaining this with a lack of junk-DNA in the engineered viruses, or perhaps some specific promoter or terminator that is known to be used by the designing aliens. A clever group of scientists should be able to anticipate these problems, however, and mask them within the genetic code. Any other ideas?

I am a biologist, so hit me with whatever science you like, but I am not an expert in genetics or diseases which is why I would like some feedback.

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  • $\begingroup$ Welcome to Worldbuilding! $\endgroup$ – JDługosz Nov 21 '17 at 5:56
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    $\begingroup$ Welcome to Worldbuilding, if nobody did that already! While every Stack Exchange site has its own distinct differences, Worldbuilding is “more different” in some ways. In particular, you ought not Accept an answer before waiting at least 24 hours. A full explaination can be found on this meta post. $\endgroup$ – JDługosz Nov 21 '17 at 20:57
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    $\begingroup$ Do the aliens even need to hide the fact that the killer-virus was engineered by them? Knowing it's engineered won't help the victims much with creating a cure. $\endgroup$ – Philipp Nov 22 '17 at 0:11
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    $\begingroup$ Yes they do need to hide it as best they can. Murder is illegal in their society, as it is in ours, but this is a plan being carried out in secret, so they can't let the general public found out. $\endgroup$ – JVerse Nov 22 '17 at 2:13
  • $\begingroup$ Might wanna check this worldbuilding.stackexchange.com/questions/70252/… $\endgroup$ – Nick Dzink Nov 22 '17 at 21:48
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I think the best answer might be the one you supplied yourself -- that is, the lack of junk DNA. The engineered virus might just be too ... slick to be natural.

Another thing to look at is the shell of the virus (if it has one). Many viruses have a protein shell. Perhaps the alien virus' shell has unusual compounds not seen elsewhere on Earth, perhaps it has some non-protein structures mixed in. Check here for some coolness: https://en.wikipedia.org/wiki/Capsid I like this option because the shell is discarded upon cell entry, so it can be almost as weird as you want without making the DNA too weird.

You might go the other way; maybe the alien gene engineers did use their "native" viruses and for economy's sake (hey, there are a lot of aliens to destroy, and we're on a budget) they didn't cut out the junk DNA. So that junk DNA might contain exotic nitrogenous bases, not just your boring Earth adenine (A), thymine (T), guanine (G) or cytosine (C).

Admittedly, this is a toughie, because a virus is a pretty cut-to-the-bone pseudo-organism. There's not much you can change about it and still have it work to infect Earth cells. I'd thought about making the phosphate groups that comprise the side of the DNA "ladder" (the bases ATGC are the rungs) have a different structure, but then the DNA polymerase might not be able to grab on and unzip...

Short story -- the easiest methods to make your virus still work but be exotic enough to call attention would be no junk DNA, or an exotic shell.

Update after comments: There was a question as to whether viruses have junk DNA at all. I couldn't find a definitive answer (I'd made the assumption), because the notion of "junk DNA" is being challenged right now. I did see this interesting article ( https://www.ncbi.nlm.nih.gov/books/NBK8439/ ) which discusses classes of mutations in viruses which do not cause a change in protein expression, so I'm hopeful.

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  • $\begingroup$ «exotic nitrogenous bases, » where would the cell get those to build more virons? $\endgroup$ – JDługosz Nov 21 '17 at 5:54
  • $\begingroup$ Are you sure viruses have junk DNA? $\endgroup$ – JDługosz Nov 21 '17 at 5:55
  • $\begingroup$ @JDługosz great question, I've edited answer to discuss the second one. To the first one, I'm assuming that the requisite elements are hanging around, but just not used in typical DNA (just like RNA has uracil instead of thymine). $\endgroup$ – akaioi Nov 21 '17 at 6:21
  • $\begingroup$ Are there such bases used in the cell for other purposes? You'll also need the machinery for assembling those when duplicating or reverse transcribing. $\endgroup$ – JDługosz Nov 21 '17 at 6:41
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    $\begingroup$ To add some references 1) "Junk" DNA tends to refer to non-coding DNA which can have a function ( news-medical.net/life-sciences/What-is-Junk-DNA.aspx ) . 2) Viruses can have non-coding DNA but it tends to have a function and is therefore nessesary to the Virus and not junk genesdev.cshlp.org/content/29/6/567.full $\endgroup$ – P Chapman Nov 21 '17 at 17:37
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A natural virus will show a family resemblance to other strains. There will be a few changes that explain why it suddenly appeared to us (effective virulence or zoönosis). We will be able to see an evolutionary path from old to new. Think of running a diff between versions: you can change a single code, delete runs, insert runs (if you find the source of the insertion: duplicate other parts or a different virus or from the host?), cut/paste from one place to another.

Now that is really a roll-up of many individual checkins. Just as with code, every checkin must work and be infectious and reproduce. With some pondering, we can figure out the individual checkins and some order dependencies among them; with more work (and searching for more wild strains) we can figure out that something was changed and changed back later, enabling the versions inbetween to function.

Individual changes are small changes.

Furthermore, nature is a sloppy engineer, as the expression goes.

Consider the revision-control repository analogy again. Look at a codebase history, and you can see lon stretch where it’s stable, then spot changes made by maintenance coders just fixing the immediate cause of a bug without deeper understanding of the code. Then a checkin where an engineer was tasked to really update it. It's fundamentally a different appearance in the diff, and quite obvious.

So, if the virologist finds that the code has been refactored, cleaned up, and entirly new chunks added (rather than copied from somewhere else), it will be obvious that it was intelligently engineered.

And that is how you can explain it in the story. It’s obvious to the virologist, and she trys to articulate her reasoning to others.

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    $\begingroup$ +1, but "virility" is something men (should/ought to) have. "Virality" is something some memes have. Viruses may have "virulence" and "pathogenicity". I would have changed the word but I'd don't know whether you wanted "pathogenicity" (the ability to infect induce disease) or "virality" (degree of severity of the disease). $\endgroup$ – AlexP Nov 21 '17 at 21:49
  • $\begingroup$ @AlexP interesting — Latin vīrus/vīrī (poison) is not related to vir/virī (man) even though the declined words can have the same spelling. $\endgroup$ – JDługosz Nov 21 '17 at 23:19
  • $\begingroup$ Lewis and Short relate vīrus (long ī and neuter) to Sanskrit visham and Greek ἰός (hiós), which means that the ancestral stem would be *wis-o-, which, according to Wikitionary, meant "fluidity, slime, poison". On the other hand, vĭr (short ĭ and masculine) comes from *wiros, which always meant "man", hence in Modern English werewolf "man-wolf". But I suspect you already knew this. $\endgroup$ – AlexP Nov 22 '17 at 0:01
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Do it the way computer security experts identify digital viruses. These aliens have certain patterns for their virus they use again and again.

  • The genetic code how the virus blends into the immune systems of various species and how it hurts them is different each time.
  • The code which holds it all together, and how the virus replicates itself, is exactly the same.
  • There might be "kill switches" to prevent species-hopping or to make the virus self-destruct after a certain number of generations. This could be replicated as well. Perhaps that's integrated with the replication code -- this virus is really resistant to random mutations, except for the stealth shell which is allowed to mutate normally (or even more quickly) to defeat vaccines.

What is the likelihood that a dozen different viruses, all from different species, have exactly the same sequence several kilobases long??

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Thing is viruses are a part of an established ecosystem. Your viruses are used for genocide, therefore they have to be terribly effective at three things:

  1. Virality or how quickly and effectively it spreads among specimens.
  2. Lethality or how effective it is at killing infected specimens.
  3. Tenacity or its' ability to persist despite immunity adaptations and consious attempts to cure it.

First two already contradict each other if both have to be achieved in a short time frame. The third would make the virus too complex or alien to the ecosystem at question.

In order to achieve all three goals your virus would have to be way too different from current or past stamps of viruses and therefore would not have an evolutionary lineage marking it as artificial.

From an analysis perspective it would look like: "Well we had that flu(virality) stamp that was pretty nasty, but 'suddenly' it acquired the traits of ebola(lethality) and hiv(tenacity). Something ain't adding up, man, I think we should discuss this issue at the Galactic Council."

You can try and bypass this by saying that there already exists a mega virus that posses all three traits and only changes targets in a single evolutionary adaptation, but in such case virtually everybody would try to study it and defeat it before it targets them. Possibly they would even monitor its status making any attemepts to mess around with it result in the same consequenses as WMD proliferation.

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