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If I picked up a DNA molecule and randomly snipped out a piece with scissors what is the scientific name for the resulting piece?

I'll confess right up front that I am not an academic or professional. I am retired and write science fiction for a hobby but I like everything in my stories that can be true and correct to be so.

In my current novella I have AI searching through the entire human DNA molecule (coding and non-coding) for a piece of DNA not related to grains but to a grain viroid. I am aware that viroids only infect plants but for my story I need a piece of this viroid to have spliced itself into the DNA of grains. That will then be found in the DNA we share with grains. Like the DNA we share with chickens, fruit flies, and bananas.

In my novella the reason for this is that it is a part of the trigger sequence for human metamorphosis which then takes place over ten thousand years. Just as things like body weight, food scarcity, etc. are triggers for metamorphosis in other animals, eating large amounts of grains is the trigger for human metamorphosis in my current story. Eating large amounts of grains means the development of agriculture and thus civilization. In my fictional universe where earth-like humans are not unique but common (due to convergent evolution) the birth of a new civilization means the beginning of their end unless they can escape the confines of their planet of origin before they destroy themselves via some version of the great filter.

Metamorphosis in other animals is an evolutionary strategy that is believed to have developed for similar reasons.

The metamorphosis that is triggered in humans leads to the development of AI and robotics and the next stage of life for the species. It enables them to spread to other worlds (which our organic bodies can't do in time) just like dragonflies leaving their pond.

"Why is humanity so compelled to create artificial life in its own image? Perhaps the caterpillar feels the same as it builds its chrysalis and for the same reasons." -- quote from my story, Metamorphosis And The Messenger.

So that's the big idea. As I was writing a paragraph about this search I wanted the correct word for a random piece of DNA. Google's AI only responded with names for specific pieces of DNA like genes, bases, exons etc. So since Google's AI is not smart enough to handle my question here I am. Maybe it's just called a "piece" but if there is a proper, scientific name I would prefer to use it.

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    $\begingroup$ Not in reference to this specific question necessarily, but it occurs to me you might like our Worldbuilding stack. It exists for the express purpose of helping writers, artists, game-designers etc. design their fictional world. (Take their tour, read-up in their help centre before posting.) $\endgroup$
    – Jiminy Cricket.
    Commented Jul 26, 2022 at 20:00
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    $\begingroup$ Hi NetCentric, and thanks for posting your question. A few things: (1) you say "the entire human DNA molecule" -- the diploid human genome is comprised of 23 chromosome pairs, so 46 individual molecules (92 if you consider dsDNA to be composed of two interacting ssDNA strands). (2) I agree with Jiminy that your question is likely a better fit for the worldbuilding stack. $\endgroup$
    – acvill
    Commented Jul 26, 2022 at 20:03
  • $\begingroup$ Thank you for suggesting the Worldbuilding stack. I was not aware of this resource but will check it out now. $\endgroup$
    – NetCentric
    Commented Jul 26, 2022 at 20:11

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If you were to literally chemically remove a piece, as with restriction enzymes or physical disruption, that would be a "fragment".

If you just mean a focal region of a genome, then "locus" or even just "region" would do.

I'm aware it's a SF premise and not meant to be super robust scientifically, but how do you see a pattern of descent in which a viroid that infected a grain (a plant) gets into a human (an animal that diverged 1 billion years ago, long before there was such a thing as multicellular plants)?

It's formally possible via horizontal gene transfer when people eat grasses I suppose, but then it's not part of the commonly inherited regions that we share with the other organisms you mention, as those branched off long before.

I suggest looking into work on ultraconserved genomic elements as relevant to the mechanism by which the "AI" might work. These methods are relatively commonplace though, not sure that they merit the buzzword though.

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    $\begingroup$ To be clear, the "piece" OP is looking for should probably just be called a "gene". It would be reasonable to say that the AI is checking fragments of DNA for a gene introduced by a viroid, if taking all the premises as reasonable. $\endgroup$
    – Bryan Krause ♦
    Commented Jul 26, 2022 at 20:26
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    $\begingroup$ @MaximilianPress I think of "locus" as a position in a genome rather than something functional. Even if the product is unknown (or if it's unknown that there's even a product vs a regulatory role) wouldn't gene be better? $\endgroup$
    – Bryan Krause ♦
    Commented Jul 26, 2022 at 20:37
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    $\begingroup$ @MaximilianPress I think I'm leaning newer, rather than older, the definition that eg Wikipedia captures as "a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression"; specifically that final 'or'. But I suppose it's still unclear whether OP's chunk should be a single gene, or multiple, or what... I still think of "locus" as being a bit more like a street address with reference to a chromosome. $\endgroup$
    – Bryan Krause ♦
    Commented Jul 26, 2022 at 22:53
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    $\begingroup$ Of course there's a lot of overlap there, too, because if a building is on fire at 11 Wall St., whether you refer to the building or refer to it by address you still mean the same fire. $\endgroup$
    – Bryan Krause ♦
    Commented Jul 26, 2022 at 22:54
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    $\begingroup$ @BryanKrause Yes I think that we broadly agree, I find the wiki def'n to be a bit too vague but that's really a matter of taste. When we talk about the kind of algorithms that people use for this purpose I think that a "street address" is certainly appropriate, to follow your analogy. $\endgroup$
    – Maximilian Press
    Commented Jul 26, 2022 at 23:04

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