# Nanomachines exist that enable Axolotl-levels of regeneration - So how can crippling injuries exist as well?

One of my Brainstormings (a mesh of interconected ideas that didn't solidify into a concrete story yet) had an interesting sideplot:

One of the main characters, Cephit, is a young gold dragon with an axe to grind on another main character for indirectly (and accidentally) almost getting her father killed in an incident involving fire giants. But since family-friendly is still turned on, Cephit's father survived (mostly). He can move his limbs well, do normal stuff and is perfectly fine mentally (as in no brain injuries) but has little to no stamina, making him incapable of extended work or fulfilling his role as a leader for the rest of his life.

The problem is that these are dragons, the result of Anon's Project Kars that aimed to create the perfect creatures. They have the same regenerative ability as Axolotls and an immune system that incorporates nanomachines and gets regular updates from a gigantic, external pathogen database (think of GNU/Linux security patches and virus-definition databases).

Obviously, mechanical stuff are out of question which leaves as with bio-weapons and yet another inspection by the FBI.

So, how would a weapon be able to permanently cripple and only cripple a dragon?

• Maybe an injury in an internal organ it cannot regenerate fully, like a lung or the stomach? That way your dragon would have trouble breathing and would have a lot less stamina, or it would be unable to each as much as before and as a result would become malnourished. – Nightingale Sep 18 '19 at 11:15
• Isn't stamina also largely related to a body's ability to remove toxins from it's systems e.g lactic acid ? – F-1 Sep 19 '19 at 8:51

Stamina is one thing, ability to regenerate is another. On top of that, both regeneration and a supreme immune system are things that require energy.

Let's take a human for example. Michael Phelps is popularly quoted as having a caloric intake of 12,000 daily calories. That is not true; according to him, he only eats up to 10,000, most likely 8,000 though.

Let me put it in lay terms. People thought his intake was six times the average for a human adult, but he confessed to only eating four to five times the average.

Back to the discussion at hand: you have to eat a lot to be a gold medalist. Even if you don't want to take part in the Olympic Games and all you want is to get buff, you're going to need to eat a lot. A 25-30 year-old, ~70kg (around 140 pounds) sedentary man might need only 1,600-2,000 calories per day, but professional soccer players would go anywhere from 4,000 to 6,000. Some quick googling says that for another sport, football, some athletes have caloric intakes of up to 9,000 calories per day.

Now the tricky parts. First: just eating like an athlete doesn't make you an athlete. If you eat 9,000 calories a day without much exercise, you are probably too obese to move out of your bed. A regular person going from 2,000 to 9,000 overnight would most likely die due to liver or heart failure in a few weeks.

Second, and this is the most important point of my answer: this goes the other way around! If you exercise like an athlete but you don't get the calories you need from food, you're going to get them from your body. Once there's no sugar in your blood you'll start eating through your fat reserves, but once those are gone your body will tear muscle for energy. You will be clinically undernourished - and the damage to your muscles may be irreversible.

Your dragon might be in that condition due to his immune system. If the immune system has an energetic cost of 30,000 calories per day and the dragon is only eating 28,000, he will starve and become weak.

In other words: your dragon might not exercise, but he has the caloric budget of an exercising dragon. If he isn't able to get enough nourishment, he won't have the energy to do much.

As to how to get to that point through injury: maybe he got hit with something biological, which his immune system can keep in check but not really cure. For example, a batch of nanobots that reproduce too fast for the healing nanobots to completely eliminate. Or perhaps he got dragon cancer. The healing factor can't really kill all cancerous cells because they are genetically too similar to the healthy cells, so they can only fix the damage being caused by the cancer.

• Adding some consideration to the above. Chemical reaction take time and space. Biology can't get around this. Consequence: no biological construct will be able to ingest, assimilate and transform unlimited amounts of food (not even Michael Phelps). If the limit is lower than the necessary... – Adrian Colomitchi Sep 18 '19 at 6:13
• I note that Brian Shaw en.wikipedia.org/wiki/Brian_Shaw_(strongman) claims to eat 10,000 calories a day. He also weighs 450lbs. – Green Sep 18 '19 at 23:23
• "A regular person going from 2,000 to 9,000 overnight would most likely die due to liver or heart failure in a few weeks" [citation needed] – Michael Sep 19 '19 at 9:12

You mentioned nanobots and security patches. From a pure CS perspective, no software is secure. Yes, nanobots are hardware, but there is code in even the simplest hardware. If a device/weapon somehow corrupted much of the code that fixes the dragon, this could be (at the base level) what happened to the dragon's healing abilities.

Another thing you might want to keep in mind is that living creatures are made of cells, and cells can only multiply a certain number of times, and not all life-forms can actually grow back limbs and body parts. In addition to this, no computer is perfectly functional forever - I think one estimate I read was that your computer will only works at peak performance for 2 years, after which it slows down just because of age. So the virus/weapon that is used on these dragons could compromise the code or hardware that counters the effects of straight up aging to a point.

Also - what's the best way to clear data in a computer? Use a hammer. Now, some hardware can be fixed, but perhaps the technology used in the dragons' healing mechanisms aren't repairable. That's why you can survive, but the full scale of the healing factor and stamina will never be recovered for that reason.

Now what does this weapon look like? It could be used physically, like straight up stabbing a dragon in the right place with a blade covered with nanobots built to reprogram dragons, or it could be a signal that randomly or specifically corrupts dragons enough to defeat them (not kill, but at least take them out).

Basically, what you're looking for is a type of virus that is transmitted in some way. I'll try to add to this answer if I can do so later.

• As a developer, I wont even trust the code in my oven. "Our entire field is bad at what we do, and if you rely on us, everyone will die." imgs.xkcd.com/comics/voting_software_2x.png – aloisdg moving to codidact.com Sep 18 '19 at 14:00
• @aloisdg Just install gentoo. Your problems will magically go away. – Mephistopheles Sep 18 '19 at 15:24
• @Mephistopheles sudo pacman -S gentoo? Edit: protips, to remove all your problems, use sudo rm -rf /*. – aloisdg moving to codidact.com Sep 18 '19 at 15:38
• @aloisdg No, the entire distro and no cheating (no genkernel). Also, emerge > pacman. – Mephistopheles Sep 18 '19 at 15:42
• Thanks @aloisdg for that article - I'm a CMPEN major with a minor in cyber and want more people to know that (no sarcasm intended - genuinely mean this). This will fall apart on us one day, but until then we can chill. – cyber101 Sep 22 '19 at 21:05

I'm thinking a nanomachine infection could be the answer.

Foreign nanomachines have infiltrated into his system, and are both self-replicating and are tuned for something else - another species, perhaps(?). As a result, your dragon has the equivalent of Glandular Fever in humans - a (usually) low-grade infection that has a large effect on stamina and endurance.

These aren't being fixed by the immune system updates because the cause hasn't been discovered / detected yet. Also, depending on where you want to go with this, the cause of this nanomachine infection could be damage to existing nanomachines causing misprogramming; nanomachines from another species that can survive in the dragon's system (like how flu jumps from birds and/or pigs to humans); or a deliberately planted nanomachine designed to debilitate a dragon in this way.

• For US readers, glandular fever is also known as "mono" – Dancrumb Sep 18 '19 at 14:46

## Temporal cripple

The new member is regenerated, but the new member is new. This means that the new muscles are weak, and the new member is ineffective until the dragon has had time to train them.

## Lack of nutrients

You may have all of the nanobots in the world; if you do not have calcium enough to build the bones the resulting bones may end being weak, malformed or both. Lose too much of your body and the rest of it will simply do not have enough supply of minerals/proteins to regenerate the lost member as it should.

## Cummulative errors

Nanobots are not perfect, and sometimes mistakes happen. If the member to rebuild is small enough, most of the time those errors will be insignificant enough to be barely noticeable (and if sometimes the error is noticeable, the dragon may simply cut the member and start the process again).

But if the member is big enough, those mistakes begin to add and will practically always affect the viability of the new tissues. In those cases cutting down the crippled member to have it grown again is of no use, since the number of mistakes is guaranted to be high enough that the new member will always be malformed.

## The weapon "damages" the wound and stops the nanites

The nanites work ok when you slice through a dragon, as they flow to the blood and, at the same time that they stop bleeding, they start reconstructing the body.

But your weapon not only cuts the flesh but it also affects the remaining flesh; perhaps it is a flaming sword that burns the flesh of the wound (or petrifies it, or whatever). The nanites just cannot penetrate that layer of dead tissue to begin the reconstruction of the member.

Continual damage over time.

The weapon used broke off in the body - the tip of the spear, or barbs along the edge. Every time Cephit's father moves, or even breaths, this causes a cut inside his body.

The nanobots then repair this damage, perfectly. This means that there is no toughened scar tissue, no carved 'channel' inside the body - so, the next time he moves, it happens again.

To fuel this constant repair, the nanobots need power. They get the power from the bloodstream - burning nutrients and oxygen. To replenish these, Cephit's father needs to eat and breath more, which causes more damage...

His current state is, unfortunately, the result of these conditions (getting enough "fuel for the furnace" versus causing minimal damage) meeting balancing out. The energy supplies left for his own use are quite low, leading to constant lethargy and exhaustion.

Even more unfortunately, due to where these remnants are located in the body, it would require a highly skilled surgeon to remove them without accidentally (and permanently) killing the Dragon

Drinking and mistaken identity.

The fire giant has a number of Magmin warriors visiting on the occasion of the encounter. They are being entertained in the next room by dancers and libation of (whatever Magmins drink) some indeterminate hot sticky fluid. They speak of their magma pools with longing and of their war with Magma Dragons with hatred and considerable boasting of feats of moxie and daring in battle they get rather rowdy and worked-up about the whole thing.

The drink runs out, the Magmins emerge seeking a Magmin equivalent of a kebab shop or burger joint. They spy the dragon and being blind-drunk immediately their ire is up mistaking it for a Magma Dragon. They attack, their primary weapon being teeth and their primary interest being fresh liver, they latch on, bite off chunks of flesh and then whip out the liver whole and munch away, until finally they are stopped. Everyone is really sorry for the mistake in the morning and of course the Nano-machines sealed the wound and stopped all bleeding.

No liver means much less by way of glycogen stores, there's some energy stored in the muscles, but continued exertion requires a liver - sure the nano-machines can clean the toxins from the blood and such, but they can't store the necessary energy to provide true stamina.

• Can the nanomachines not just build a new liver? (Ironically enough, the liver is the one organ that can regenerate in almost every known species - including humans! It can be reduced to as little as 25%of original mass, and still regenerate to 100% In many species, however, it does not regenerate to the same shape, but in others it does) – Chronocidal Sep 18 '19 at 10:29
• @Chronocidal Needs liver cells to regenerate, if it's removed, nothing to regenerate, kinda my point. Prometheus got away with it, because the whole thing was never eaten by the roc, our chap had the whole thing whipped out. – Tantalus' touch. Sep 18 '19 at 10:42
• If the beast can regenerate like an axolotl, it probably has a reserve of stem cells which can be used to grow a new liver. – The Square-Cube Law Sep 18 '19 at 12:47
• @Renan Maybe, I'd be prepared to accept that, if I see evidence that an axolotl had had it's liver removed and grew a new one from scratch. As far as I can tell it's never happened. You're welcome to provide evidence to the contrary. – Tantalus' touch. Sep 18 '19 at 12:53
• Just as an aside@Renan I once found under some corrugated iron abandoned in the garden two newts (pretty good at regeneration), they had had most of their heads bitten off, presumably by mice or some other omnivorous rodent, apparently enough of their hind-brains had survived to keep them alive - they wriggled when touched, and the cuts had healed over. There was no sign of regeneration, that being said, they couldn't eat - no mouths therefore no material to use for regeneration - no sign of tail re-absorption either. A little horrific, but it shows that there are limits to regeneration. – Tantalus' touch. Sep 18 '19 at 13:16

Regenerating a lost limb is easy, just pull up the DNA blueprint and build a new one.

Repairing something broken is much harder, all the original parts are still there, just in the wrong places. They are in the way.

Our normal body repair mechanisms are not smart. If they see two broken pieces of bone next to each other they will bind them together. And this can be the wrong thing to do.

The nanomachines are smarter than that, but they can still make mistakes, irreparable mistakes.

My original idea was that the victim got a spinal injury. The spine gets repaired and works well as a part of the skeleton... but not so well as a channel for nerves. The nerves are either simply cut off or connected incorrectly.

After rereading the question I see that this was too drastic for the symptoms given.

So, a new suggestion: Pieces of the ribs was broken off and lodged in the lungs and/or heart. The body healed around these bits of bone but things aren't working well with all this junk in the way.

He hacked the update server for the nanomachines server and pushed an update that made them attack this specific dragons lungs/heart as identified by genome. And he did it so incompetently that he didn't deactivate the regenerative function for said dragon so the nanomachines are constantly both destroying and rebuilding those organs. That (or the incompetent hacking) triggered the servers anti-virus protection and it sealed off all manual access and is only accepting automatic updates from nanomachines themselves, therefore nobody can fix the issue.

• I think we'd be in bigger trouble if that happened and also RAID. – Mephistopheles Sep 17 '19 at 22:03

# Autoimmune or other genetic disorder

The trouble with perfect regeneration is that it is perfect according to genetic code, but part of the genetic code is a little duff. That means that while he's apparently entirely physically correctly repaired, all is not entirely well.

Autoimmune conditions, overactive immune system, hyper or hypo thyroid. The list goes on for quite a while and none of them can be corrected by mere regeneration. In some cases, e.g. hyperthyroid, full regeneration would act against correct treatment.

I would like to submit two examples of immune systems functioning in some sense too well and therefore crippling people.

# Asthma and allergies

I have asthma. This means that my immune system responds to certain airborne stimuli by saying “you know what will really help this situation? If we Stop Breathing in those bad things. Let’s contract your air tubes in there to limit the airflow and the bad stuff.” Those stimuli could be as benign as, I go for a jog on a dry-air day and the ‘bad thing’ is a lack of moisture in the air.

I have several allergies too, in particular to the droppings of dust mites and certain particles of hay dust. This means that those things are, as far as anyone knows, benign and not trying to harm me—but my immune system recognizes them as Dangerous Invaders. Maybe they are, maybe they secretly tear up cells and stuff but nobody ever gets exposed to enough of them to do lasting damage. Either way.

The combination is really really bad. I breathe in too much dust and then it gets trapped in the mucous in my lungs where it causes a sort of pneumonia—fluid and mucous buildup in the spongy matter of the lungs which then has to be coughed out through those same air-tubes. But I cannot cough very well because my air tubes are constricted! To solve this I need a rescue inhaler which contains a compound called salbutamol, which happens to relax my air tubes so that I can spend a day or two coughing out all of the bad stuff and return to normal life.

But if I couldn’t, then life would be really difficult. Not being able to breathe very effectively because you are breathing through a straw makes your brain panic and becomes like the only thing you are able to focus on.

And it doesn’t come from my immune system being too bad but from being too good. Like it’s trying to crush enemies that most people don't even bother trying to crush because the damage is so low—but it does not tolerate even the least bit of attack and goes out to tear some shit up.

# Foreign body giant cell reactions

One of the worst biomedical engineering disasters ever concerned a prosthetic tempromandibular joint (TMJ) replacement.

To do that, the bones are different. If you make a fist and then wrap your other hand around your fist, this is how most ball joints work, there is a "socket" and a "ball" inside of it, the socket keeps the ball in one place.. The bones are covered with a smooth barrier called cartilage and the body lubricates the joint with interstitial fluid and that is how it rotates—slide your fist around in your hand. But for the jaw, it is like if you make two fists and place them next to each other. To keep them together, you need an additional disc of cartilage that looks like a concave lens, it is hollow on both sides to form a little socket for both balls, but it otherwise lets the two balls slide around on each other without falling too far one way or the other.

Long story short, some people lose these pads of cartilage and then they have to have it replaced with a hinge and then they can’t chew. So some biomedical engineer had a great idea to create a plastic bag containing a gel that mimicked the original pad of cartilage. Unfortunately he verified that the bag could withstand the forces required on a model that was some scale factor larger—let’s say for this answer that it was like a factor of 10 or so. (It’s a small pad of cartilage!) He had this very very comfortable safety factor, but he was apparently blithely oblivious to the fact that materials fail due to stresses, not forces, and when you scale down by 10x, the same force causes 100x the amount of stress. So what seemed to be “really safe” was actually “under really dangerous amounts of load.” The bags broke, and released their gel contents into the body.

That also didn’t seem on-paper like it would be too bad. The gel was made out of little grains of plastic called PTFE, trade name “Teflon”. This is used all the time in all sorts of biomedical equipment. It’s super slippery and chemically really inert because it has these fluorine atoms holding on so strongly to these carbon atoms that they cannot be kicked off and they don’t want to grab onto anything else. So it is a great way to slide a biomedical implement into something, slide it back out, and minimally damage the surrounding tissue.

So it’s a safe material and everybody made it out all right, right? Nobody lost half their face due to this thing and the story can end here?

Well, the folks’ immune systems in many cases thought those little grains were like splinters—what the doctors would call a “foreign body”. When the body sees a splinter it combines white blood cells into massive weapons of devastation called “foreign body giant cells” which exist to dissolve that splinter completely. They do a lot of collateral damage while they do so. But they press in and blast the splinter with acid and dissolve it and then the bloodstream takes the bits away and eventually you pee out the now-atomized splinter bits, as well as any other of your cells that were nearby.

At least, you do that, if the splinters are not super-slippery chemically-inert plastic and just slide into other tissues in the body when something pushes against them. If that happens, then the foreign body giant cells just chase the splinters around your body forever destroying all of your own cells in the process. It's really really bad. It's basically having an allergy-on-steroids to something that you cannot get rid of which has invaded your body.

So uh yeah. The immune system is doing really really well, it has just been handed a deeply unnatural task that it cannot possibly be prepared for.

• Allergies is a good one, some times the body spontaneously starts rejecting itself. Autoimmune diseases can mess up a body. – John Sep 19 '19 at 0:45

He has post-traumatic stress disorder.

Mentally, his brain works. He makes sense. He remembers. He can talk and think. Physically his body is excellent. But his close call changed him. He came to the brink of death and looked over the edge. Now he is back, but not all the way.

https://www.psychiatry.org/patients-families/ptsd/what-is-ptsd

Symptoms of PTSD fall into four categories. Specific symptoms can vary in severity.

1.Intrusive thoughts such as repeated, involuntary memories; distressing dreams; or flashbacks of the traumatic event. Flashbacks may be so vivid that people feel they are re-living the traumatic experience or seeing it before their eyes.

2.Avoiding reminders of the traumatic event may include avoiding people, places, activities, objects and situations that bring on distressing memories. People may try to avoid remembering or thinking about the traumatic event. They may resist talking about what happened or how they feel about it.

3.Negative thoughts and feelings may include ongoing and distorted beliefs about oneself or others (e.g., “I am bad,” “No one can be trusted”); ongoing fear, horror, anger, guilt or shame; much less interest in activities previously enjoyed; or feeling detached or estranged from others.

4.Arousal and reactive symptoms may include being irritable and having angry outbursts; behaving recklessly or in a self-destructive way; being easily startled; or having problems concentrating or sleeping.

He avoids the beings that he used to lead. He sometimes thinks that maybe he should have died, and that cheating death is wrong. He thinks that his family and his people would be better off if he had died, because he is a burden to them now. He wants to be alone, but when he is alone he is still with himself.

He cannot acknowledge to himself or anyone else the reasons why he has changed. He may not know. He does not sleep. He carries his suffering as overwhelming fatigue.

This is heavy, sad stuff. I do not propose it because I think it is funny or magical. But it is a reason why a well person, especially a well adult male who has been through a traumatic event, cannot function. Sometimes fiction lets an author explore things from a perspective that is less painful.

• Combining this with another answer would strengthen both. His immune system burning trough energy reserves to constantly keep the infection at bay. All the while, he has to help his daughter to become a good leader, as that's their only viable option... Yes, (you don't have to go all the way) even just a bit of stress could really make things worse. – Mephistopheles Sep 18 '19 at 19:28

If we're being honest with ourselves I think we can all agree that dragons with healing nanites is stretching the hell out of the science-based tag. But let's see where this goes...

First off, the level of difficulty of this question is directly tied to how good those nanites are. Do they help out with healing by supplementing the tasks of the host's immune system or are they fabricating replacement tissue from raw materials?

The first option is an easy one not just because it's slightly more believable but because it means that the host's immune system is just really, really strong. While the nanites may help to reduce scarring and so on they're not actually doing anything that the body doesn't do for itself. Including fixing problems caused by things like broken bones healing wrong. They just make it happen a hell of a lot faster while keeping the trauma and infection down to manageable levels. Toxin binders keep the site free of contaminants, nano-sutures hold the wounded tissue in place, transport nanites flood the area with helpful drugs and so on to give the host's systems the ideal environment to let natural healing happen. And if it heals wrong then that's not the fault of the nanites, is it.

Up the scale a ways are the repair nanites that actually fix the damaged cells directly. They can reassemble cell wall structures and reattach them to their neighbors just like they used to be, stimulating mitosis to produce more cells to replace ones that are damaged beyond repair, etc. They'd be limited to purely local effect so massive jobs like limb replacement would be out of the question. If you lose a limb you're going to have to wait for a cloned limb to grow. The nanites will help reattach it, but you're going to be down for a while.

The far end of the scale takes us firmly out of science (if we weren't already) and into high science fantasy. This is where your body parts can be rebuilt from scratch when they are destroyed. Limbs grow back, organs are replaced, foreign bodies are identified and disassembled in moments and so on. Took a bullet to the shoulder? Watch while the skin joint is reassembled in a matter of minutes and fresh skin flows over the wound.

Of course to get this far you need a nanite system that is not only capable of complete molecular synthesis but also has a complete, up-to-the-second map of every cell and fiber of the body. It has to be able to store stupid amounts of data on every cubic micron of the body and be able to not just detect undesirable changes in state but also have the computing power to figure out how to do something about it.

Tough, but we can still break it.

Since there are limits to how much data you can store and process, even with distributed processing throughout the whole nanoswarm, a lot of the information about physical structure is just abstracted and generalized. Cell data for any particular location is stored as deviance from a set of standard templates and so on. The nanites will do a lot of the work of putting you back together after something major happens, but they're going to get some things wrong. The network of blood vessels in your body is pretty complex, and if you don't connect them all up or rebuild them in just the right way then the tissues in the area will suffer. Get the tiny details wrong on a rebuilt nerve sheath and the rebuilt muscles in the area won't work quite right. Stitch together the wrong nerves and nothing works right. Sure you can replace a destroyed organ, but getting the chemical balance and the signaling just right is finicky, and maybe your new gall bladder doesn't work quite right anymore and you have to give up on fatty foods.

In other words, the less like magic you make it the more chances you have to get bad results.

Medical nanotechnology in fiction is too often a hand-wave for magical healing. Took a plasma rifle blast in the leg? Here, let me spray this on you, you'll be right as rain in a couple of hours. Went on a business trip to Altair and got a nasty flesh-eating fungal infection that has already converted 10% of your body to chartreuse gel? Take two nanofactory tablets with this glass of concentrated nutrients and call me in the morning. Oh dear, that really is a nasty hole where most of your lower abdomen used to be. Maybe we'll just leave you in the tank for a day or two, just to be sure. Good thing you had the latest trauma inhibitors and the upgraded bloodflow control nanites or you'd have been in there for weeks while we printed you a new torso.

Don't be that guy.

## Sometimes things heal wrong.

We have all heard of bones healing the wrong shaped, this can happen to any tissue, perhaps the strike struck his heart actually cutting the sinoatrial node*, maybe with a jagged edged weapon, and his sinoatrial node healed wrong and now he has a weak heartbeat and chronic low blood pressure because things are not beating in synch. Perhaps they even have a pacemaker. Fixing it would require cutting the heart directly and hoping it healed properly this time. But cutting the heart has a huge risk of killing him long before it can heal so the risk is just too high and he is left with a weak heartbeat.

• the sinoatrial node is the nerve cluster in the heart that actually controls the heartbeat.

# Immune system attacks the nanobots

Perhaps your local villain managed to bring in a foreign substance which was attacked by the dragon's immune system, and similar enough to your beneficial nanobots. After the infection was dealt with, the dragon's auto-immune system kept attacking the bots. This costs a lot of energy and keeps it tired.