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This story takes place about 300 years in the future and humanity has since come into contact with hundreds of alien races, you get the picture. Basically, I have this character who is half human and half alien, but the issue arises in that her alien heritage was an infamous and feared race thought to have gone extinct years ago. This puts a pretty hefty bounty on her since she possesses said race's key traits. I won't get into all the details, but this begs the question of "why go to the trouble of trying to re-capture her if cloning is an option?"

Based on what we currently know about cloning (or theorize), is there some biological/genetic phenomenon that would render her unable to be successfully cloned?

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    $\begingroup$ You cannot clone a mammal unless you have a suitable mother, or at least very detailed knowledge of how the processes which the mother performs work. If all the members of that feared race are dead, and there are no closely related species, then cloning would be successful only if there was some sort of very thorough knowledge of how the development of a zygote proceeded. For example, our present knowledge about the development of a human from a zygote to a newborn is very very very far from the required level of detail; we couldn't even built an artificial womb for ourselves. $\endgroup$
    – AlexP
    Commented Apr 5, 2020 at 19:38
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    $\begingroup$ @AlexP If the character is half human and half alien, that implies a human would work as an acceptable surrogate because the two species have interbred before. Indeed, that might work better because all one needs is a tissue sample and they don't have to risk antagonizing someone with the traits that seem to make her dangerous and just raise a clone to do their bidding. In fact, they could even duplicate the alien half of the genome and remove the human half to produce a full-blooded alien rather than someone who is only half alien, if degree of alien DNA is a factor. $\endgroup$
    – user2352714
    Commented Apr 5, 2020 at 20:04
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    $\begingroup$ I think with an alien-human hybrid you are probably already leaving science-based territory unless the aliens are pretty much human anyway $\endgroup$
    – jk.
    Commented Apr 6, 2020 at 15:15
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    $\begingroup$ I think the first question that needs to be asked is, "Why do they want to capture her at all?". As opposed to, say, just having her assassinated. That's going to be a big driver for answers. I mean, if the potential captors want to put her on trial for "crimes of her ancestors", cloning her seems... a bit much. If there's some gene-locked warships, and they need them soon, then the "too lazy" answer seems appropriate. Is cloning even legal in the wider galaxy, or even locally to the captor species? $\endgroup$
    – Clockwork-Muse
    Commented Apr 6, 2020 at 17:21
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    $\begingroup$ since this is science-based, you do realize that at our current understanding, no aliens could interbreed with humans. or let us say, the chance of any alien race being able to breed with human is inexplicably impossible. I mean, consider Earth as it is, animals can't interbreed even if they are only somewhat genetically different. good luck finding aliens which happen to share almost all genes of the humans. $\endgroup$
    – Gnudiff
    Commented Apr 6, 2020 at 21:44

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The DNA is just the DVD, without a DVD player it is useless.

If the characters mother is the alien then its all fine.

The technology to clone a creature has existed for a few years, but that just means putting their DNA into an embryo that still needs to be carried to term in a woman. An artificial incubator (like in Star Wars) may be in principle possible but they are so complicated that I suspect they will never be invented.

So someone takes this character's DNA. They check it, it has a mix of human and alien. They place this in a human embryo, in a human woman, and it miscarries. It could be that this specific mix of alien/human just cannot be incubated inside a human. (Perhaps an alien Fetus needs some specific nutrients the human body does not produce). Our original character avoided this problem by having an alien mother.

In order to make another person with her powers you would need a alien female to carry the baby, and if these aliens are considered to be extinct and no one can find one then their is no risk that another copy of her could be made.

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    $\begingroup$ @nick012000 He's not assuming, he's proposing. His solution is that even a clone would need to be grown inside a female of the alien species. Not a tank, not a human female, not anything else. $\endgroup$
    – Jemox
    Commented Apr 6, 2020 at 10:38
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    $\begingroup$ I would also add that, even if you wanted your setting to have advanced incubation tanks for growing human embryos, it is quite plausible that no one would have any idea how to build an incubator that would work on some weird alien hybrid, especially without being able to study any members of the (supposedly extinct) alien species. $\endgroup$
    – Dast
    Commented Apr 6, 2020 at 11:43
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    $\begingroup$ Current Research indicates that not only the DNA, but also the bacteria living in the mothers womb and bloodstream have a huge impact on the embryo (one example is the human digestive tract, which could not be reproduced without external bacteria cultures) - so it is plausible that the Alien mother transfers some symbiotic bacteria to the embryo while pregnant, without which it is not able to survive. For the alien these bacteria might even play a big role in the embryo even developing at all - with out them it never survives the third month. $\endgroup$
    – Falco
    Commented Apr 6, 2020 at 12:10
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    $\begingroup$ Falco's comment has the important point that really answers the question. When your body develops as an embryo you aren't just creating a body with your cells, lots of microbes, antibodies, nutrients, etc flow into you through blood that complete your body. That's one of the existing reasons that cloning is difficult, in fact. So assuming the mother is the alien, said race being extinct would mean it's impossible to figure out all the godzillion things you need to supply the cloned embryo for it to be complete. $\endgroup$
    – Chaffee
    Commented Apr 7, 2020 at 6:02
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    $\begingroup$ @Falco A bit like "Schlock Mercenary"'s insectoid "Kreely" species: unless infected with a specific bacteria while young, they grow up non-sentient. Some specific trait that they require from the aliens may require an external stimulus/catalyst to manifest, even if it's in the DNA $\endgroup$
    – Chronocidal
    Commented Apr 7, 2020 at 9:30
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It's not that they can't clone her, it's that they're too lazy

The one thing no cloning method we know of has ever been able to do is produce clones that are the same age as the original donor. When animals have been cloned in the past, they are born as infants and slowly grow to adulthood the same as any other organism. No one has been able to find a way to "speed up" aging in an appropriate way so you have a clone you started growing a few months ago that is the same age as the adult donor. So if you want to clone a half-human, half-alien and have them do things for you that the adult individual can do, you have to wait the necessary time for them to grow to adulthood.

For humans that's really fricking long, about 15 years or so unless they just need their thumbprint or DNA to unlock something. Or the bad guys can just kidnap the already existing adult individual and threaten them into doing their bidding because they're lazy and don't want to wait the 15 years until their clone reaches a physically mature or near-mature state, nor expend the time and effort into raising that clone into developing an emotional bond with them so they will do as they say.

This has the added benefit of making your antagonists look more villanous, as taking inefficient shortcuts that harm other people rather than doing it the drawn-out, but more moral and efficient way has a side effect of enraging audiences (in a good way, as in they hate your villains more).

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    $\begingroup$ If the villains are powerful enough, they could do both: incubate a clone and start the 15 year process of raising it, but also search for the original with the intent of disposing of the clone if they succeed. (Even more dastardly evil points!) $\endgroup$
    – TheHans255
    Commented Apr 6, 2020 at 4:41
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    $\begingroup$ Thumbprints are a bad example, because they're not genetic. Clones wouldn't have the same fingerprint patterns even after they grow up. $\endgroup$
    – Cadence
    Commented Apr 6, 2020 at 5:34
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    $\begingroup$ "making your antagonists look more villanous" - I'm not so sure about that. Birthing and raising a child (possibly in "captivity" or isolation, as these things tend to go) only to be able to use them sounds pretty villainous. $\endgroup$
    – NotThatGuy
    Commented Apr 6, 2020 at 13:12
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    $\begingroup$ Realistically speaking, they might still clone the character in parallel to trying to capture her, as a sort of backup plan. This would take several years, so the character in question might be done with their story or even dead or whatever by the time that happens. It might even turn out to be a useful plot device at some point. $\endgroup$
    – DarkWiiPlayer
    Commented Apr 7, 2020 at 7:43
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In most (if not all) earthly life forms, every cell contains all of the genetic information needed to create the entire organism. Perhaps that is not true of the alien race which is half of your character's heritage. Perhaps that race is made of a variety of specialized cells, with the full genetic map present only in reproductive cells stored safely, deep within their bodies.

If this were the case, then cloning an entire parent from a daughter's stray blood or flesh, or from any of her sheddings or biological waste, would not be possible. The full genetic map is not present in any of those parts.

But if you capture her and very perform surgery to get at her shielded insides, then and only then will have what you need to bring back that great warrior race.

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    $\begingroup$ Interesting, in humans, it's exactly the opposite - our specialized reproductive cells which we store deep within the body are the only ones that do not have the full genetic map of the individual. $\endgroup$
    – Nuclear Hoagie
    Commented Apr 6, 2020 at 13:00
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    $\begingroup$ And they might be killing the Goose that Laid the Golden Eggs. Actually, that could have played a part in that alien race disappearing... $\endgroup$
    – Ángel
    Commented Apr 6, 2020 at 20:56
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    $\begingroup$ @JanDorniak Pretty easy to change that for an alien hybrid - many mammals reabsorb the endometrium instead of shedding it. $\endgroup$
    – Ettina Kitten
    Commented Apr 6, 2020 at 21:52
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    $\begingroup$ Mammalian (including human) red blood cells don't contain DNA. They have neither nucleus nor mitochondria. $\endgroup$
    – Hugh Allen
    Commented Apr 7, 2020 at 2:33
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    $\begingroup$ @JanDorniak Following her around and managing to capture her used hygiene products and having egg(s) caught on those products (instead of in the toilet bowl or down the shower drain) and managing to locate those specific few individual cells in the mess of blood, mucus, etc. and you have to do it all pretty quickly otherwise it's going to dry out...... But they can't catch the adult? $\endgroup$
    – user3067860
    Commented Apr 8, 2020 at 18:54
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DNA is not the same in every cell of the body. Mutations and small changes exist. In an alien-human morph, it's not unreasonable to assume that the DNA would be all over the place and vary strongly from organ to organ and location to location; simply taking a skin or blood DNA sample wouldn't provide the full spectrum of DNA required to clone a viable creature.

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    $\begingroup$ Aside from mutations it might also be worth mentioning the existence of chimeras in your answer, which can happen when a single body develops from the merging of two zygotes with different DNA, so that some large fraction of cells in the body have one set of DNA and another large fraction have a different set. $\endgroup$
    – Hypnosifl
    Commented Apr 5, 2020 at 20:28
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    $\begingroup$ Maybe add an unhealthy dose of radiation to everyone on that planet so that cells from a single part of the body aren't representative of how to recreate this exact human, or at least not the same human they would have recreated if they took the same samples 5 years ago. $\endgroup$
    – pilkch
    Commented Apr 6, 2020 at 7:18
  • $\begingroup$ @Hypnosifl I like that point: perhaps every attempt at a clone they have made came out pure-human? $\endgroup$
    – Chronocidal
    Commented Apr 6, 2020 at 9:37
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    $\begingroup$ Chimerism is a good answer. Even if you could capture the different DNA from different cell populations within the body, the way the individual develops in utero will be random with respect to how the DNA is distributed across different organs. Unlike a regular clone, you won't end up with a younger "twin" of the original, but someone with substantial variations, due to the random processes contributing to morphogenesis. $\endgroup$
    – Michael MacAskill
    Commented Apr 8, 2020 at 22:52
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The infamous and feared race was not a naturally evolved species. It was a weapon, created to fight wars for its masters.

To keep that weapon unique and to keep them from being easily duplicated by the master's enemies, they were equipped with trickster DNA.

The Trickster DNA copy-protection technique involves endowing each cell in the creature with hundreds of times more genetic information that is needed for replication, encrypting it so that each cell can only replicate itself consistently when provided with a specific RNA key. In the absence of that key, attempts to trigger replication can lead to all manner of chaos because included in that extra genetic information is the blueprint for every viral contagion know to the galaxy.

Lovemaking is a dangerous activity when a trickster is involved. You either get a kick@ss hybrid as a child, or planetary genocide. In the case of your character, her father got lucky in more than just the conventional sense of the term.

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Is it not possible, in your story, to simply make it so that "they" do not actually/yet have a copy your character's DNA? It could be that the bounty is out on her because they would like to strap her down and scan her DNA.

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    $\begingroup$ +1. You could also specify that DNA in dead cells degrades faster than from humans, so a "forensic sample" - a left-behind hair or flake of skin, would not be sufficient to make a clone. $\endgroup$
    – Hugh Allen
    Commented Apr 7, 2020 at 2:39
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Epigenetics. As cells specialise, they lose their potency, mostly because of epigenetic modifications to the genome. Genes that are not needed are silenced and packed away tightly to allow more efficient use of the genome needed for running that particular cell. There are also epigenetic modifications that are inheritable by offspring. One of the bigger roles of these modifiers is keep things such as transposable elements, strips of DNA that can detach from DNA and attach in another place or create copies of themselves that can attach into new places, locked in place and silent.

Some of the modifications governing the two cases described are different, but some like methylation have putative roles in both. To properly clone something, you need to strip the epigenetic modifications, lest you end up with developmental issues due to genetic material that has already specialised. Current cloning methods rely on finding and using nuclei from more potent cells (stem cells) with less specialisation-related epigenetic modifiers to get around this.

So, the extinct aliens have genome that is filled with transposable elements, which are contained with epigenetic modifiers indistinguishable from epigenetic modifiers accrued during cell specialisation. Strip the epigenetic elements and the transposable elements go wild destroying the whole functional genome of the species.

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  • $\begingroup$ +1, because this is a classic. Fish, reptile and amphibian DNA has to deal with substantial environmental issues. It is well known that some species can be sexually selected simply by changing the temperature their eggs are incubated at, but this still gives viable offspring. Mammal development assumes a womb and a well-regulated development environment though, and offspring are not at all robust to issues caused by problems with the mother. Starvation in Holland during WWII caused substantial problems for children born then, and even to their children, for example. $\endgroup$
    – Graham
    Commented Apr 7, 2020 at 10:26
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A similar issue was addressed in the Vorkosigan saga
Miles Vorkosigan suffered teratogenic damage due to a chemical attack on his mother while she was pregnant with him, giving him weak bones and twisted legs.

Later in the series he is cloned in a plot to replace him, but the clone came out looking perfect(because the damage to Miles wasn't genetic) and so could not be used in the plot

you could introduce some teratogenic damage to your character that wont be easily reproducible in a clone, perhaps a brain abnormality which is known because an MRI image of her brain from a medical exam has leaked.

Alternatively anything uniquely identifiable that your character has that can't be stolen or replicated, for instance an embedded ID chip that holds a private key

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Make the "hybrid" nature the key to the problem. Make the two races biologically incompatible, so that any hybrid needs to be raised in an artificial womb. In that environment, it was possible to provide two separate nutrient streams for both backgrounds.

Now, the clone would need such an artificial womb, too. That's still possible. The nutrient stream for its human (mammalian) side is no problem either. But how do you create the nutrients for its alien half? There's no documentation, nor a living female alien to study.

Also, there might be some immune system challenges during fetus development which need to be addressed, but which are impossible to work out without an actual alien to study.

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You get a baby

If they cloned your character successfully¹ they would get an undeveloped (half-)alien. Not only physically, but -most importantly- also mentally.

It might be feasible, as a long-term plan, technically. You would need to slowly² raise him, and you might end up with a very loyal servant. But initially you would have a baby you are unable to communicate with, but having those interesting traits it's unable to control. Let's suppose they are powerful telepaths, which could break into the mind of those around you. Surely, the abilities of a baby would be nothing to their parents. However, those nurses you wanted to take care of your clone, would have constant headaches, as the baby would simply throw its thoughts all around it. Oh, and a temper tantrum would end up with many casualties.

On the other hand, your character has learnt to control its thoughts, and will not let them slip outside,³ so it will not inadvertently be dangerous to people around him. You can also communicate with him in your galaxy variant of newspeak. He's unlikely to love their captors, but they could deceive / extort / torture / bribe him so he collaborates with their plans.

¹ It's not that clear, see other answers, but assuming they managed to do that.

² Did I mention how many centuries do they take to fully develop their potential?

³ Basically, it's an automatic thing for him

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Was she a natural hybrid? If not, you could check out the various ways that rat/mouse hybrids have been attempted for ideas. In particular, if the hybrid character is a chimera, cloning won't work unless they can reproduce the particular mix of both species' cell lines. In the case of a secondary chimera, you'd need to know exactly what tissues were xenografted and at what stage of development, or else your reproduction won't be the same and might not have the abilities you're hoping for - or even be viable! Furthermore, especially with a secondary chimera, you could have serious trouble getting a hold of one cell line if it's not represented in blood, mucous membranes or hair follicles. And understanding that she is xenografted and which cell lines are xenografted would be considerably harder if the villains don't have access to her to run tests on.

Furthermore, note how many of the methods that produce viable laboratory-created hybrids do so only as a small proportion of the total attempts? If only 5% of hybrids are actually viable, they could easily lack the resources to keep trying long enough to get a success, or if they don't luck out early enough, they could mistakenly assume that they've got the method wrong.

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The extinct race was feared because they were bio-engineered weapons. To prevent the proliferation of this weapon the species designers created the species as an RNA based organism vs a DNA based organism. This means that every cell division in a creature cloned from the extinct race has a very high chance of mutation and clones quickly succumb to cancer if they even reach maturity.

In fully developed specimens of the species they have a emergent body system that prevents the mutation of the cells RNA when dividing allowing it to function like a normal DNA based organism. Normal procreation of the species allows the mothers RNA replication protective system (RRPS) to prevent a fetus from mutating while in the womb until it is mature enough that its own RRPS takes over.

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Yes, Roger Penrose hypothesizes that humans contain quantum processes.

In fact, (in your story) it turns out that Penrose was on the right track.

But humans are not quite that evolved yet.

Humans don't contain quantum processes.

But that race of aliens DO include quantum Penrose processes in their brains...

Bingo.

Our half-breed heroine also includes quantum Penrose processes in her brain.

You can't clone a quantum object...

she is utterly, utterly unique and unclonable in a world where cloning is commonplace.

Great plot.

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The DNA doesn't match the body

The hybrid in question wasn't grown from DNA but actually 3d bio printed using the DNA.

In the Fifth Element, Leeloo has her whole body reprinted from a sample of her DNA

enter image description here

Now there is no reason a body couldn't be printed in a different form using the same DNA. Now if someone took said DNA and grew it out, it wouldn't give the same form and being a hybrid of two alien species, may not even be viable to survive.

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If you are talking alien, why assume they are DNA, or even carbon-based for that matter? When you say hybrid, people assume mixing humanoids through reproduction. But what if you have something like a silicon-based bacterium that creates a hive-mind from a sufficiently large aggregation of independent cells. Perhaps, this bacterium was a sentient being once, or engineered by other sentient species for some purpose (memory, war, as a tool, etc).

Now a hybrid would be something completely different: it would be a mass of these creatures living in a human host in a symbiotic relationship, giving the resulting being the sum of their powers. Part of the plot could be that this has been tried many times in the past by many species, but always resulted in spectacular death, or the bacterium taking over the whole planet or whatever. Perhaps one such experiment could be the reason the bacterium was supposedly wiped out to begin with.

This would present the motive for capture, and the inability to clone. There is simply nothing to clone. The human portion is just human, but the alien is the last remaining culture of what was once a non-carbon-based hive mind bacterial culture. No one knows how to replicate it, and if they did, creating the hybrid is something that no one has ever been able to do.

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Her DNA contains a virus.

Her DNA could encode a computer virus that when the cloning machine reads it, is infected and breaks down. Or her DNA contains a real virus that is only activated by the cloning method (by some chemical reaction or physical process used only during the cloning process) which proceeds to destroy all the genetic material in the cloning machine.

It's been (partly) done already https://www.wired.com/story/malware-dna-hack/ where researchers embedded a hack into a strand a of DNA, so when the DNA was read it caused a buffer overflow in the DNA sequencing machine.

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Her cells or DNA exist in quantum states, which makes it un-clonable.

In physics, the no-cloning theorem states that it is impossible to create an identical copy of an arbitrary unknown quantum state.

Source: https://en.wikipedia.org/wiki/No-cloning_theorem

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The telomeres in her cell's nuclei are compromised due to the cross-breeding, and therefore it is extremely hard to create a clone that will survive to adulthood. The telomeres are still there, and are still functional, however it is very hard to bring the cells back to their unspecified state (in order to clone them). She can still live a normal life span.

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  • $\begingroup$ Wouldn't this also mean the protagonist is going to die very, very young as a side effect? $\endgroup$
    – user2352714
    Commented Apr 6, 2020 at 20:57
  • $\begingroup$ Yeah, I edited my post so that she will live a normal life span. $\endgroup$
    – CheetSheatOverlode
    Commented Apr 10, 2020 at 13:19
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Something that will make her different, could be something like triple helix DNA, or more chromosomes, and the cloning machine only works on regular DNA

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Gene expression

Gene expression does not replicate the entire DNA. There are a lot of chunks of DNA that are inactive, they are not transcripted by the RNA and they do not contribute to the formation of the cells.

Gene expression is often influenced by environmental factors. For example the genes that drive the transition to adulthood during puberty are activated at a certain age, but different environmental or psychological conditions can anticipate or postpone their activation by few years. There is also the case of several chunks of the DNA that are never expressed because they are relics of the evolution and they are present in almost every species.

In your case the explanation can be that even if they have the DNA they don't know the environmental conditions that triggered the expression of the right genes. Nurture matters. To replicate the alien traits they not only must get the DNA from your character, but they must also find out how she grew up, what environment she was in when she was a toddler.

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one: Androids can't be cloned.

two: Scientists are already well on the way to growing laboratory outer ears that can be transplanted onto people who lack, or have lost, their outer ears. The trick is to create a scaffold for the relevant cells, seed it with collagen, and seeding the resulting collagen scaffold with cells. https://www.popsci.com/science/article/2013-07/artificial-human-ear-good-shape/

In three hundred years' time, might it not be possible to fabricate an entire person in this manner? If the resulting manufactured person were seeded with cells from a number of different people, cloning the manufactured person would not be practical. Also, since the collagen scaffold was not a product of DNA replication, cloning a manufactured organism would be doubly impractical.

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