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Technological Transformation Methodology
Transformation in Fantasy is easy. 'Poof' and it's done, or alternately one may need to say a magic phrase such as 'Hsif a tewN ekaM'. In Science Fiction it is much more difficult, and that's even ignoring Clarke's 'Any sufficiently advanced technology is indistinguishable from magic.' Thus, though my personal transformation was more of the fantastical 'poof' type, I offer a selection of possible and not so possible technological transformation methodologies for your writing pleasure.
Exterior Transplants: This is going on currently in a limited manner and involves plastic surgery and surface transplants to transform one. Currently this is limited to modifying the appearance of human flesh and transplanting artificial substances such a fishing line to form cat whiskers. However, it is possible that eventually surface transplants could include genetically modified fur that could be grafted on as a new skin, either artificial cybernetic or genetically engineered eyes to give enhanced vision, and a tail. Of course, sticking stuff on is easy, getting the human brain to actually make use of the stuff is a lot tougher. The human brain is a badly understood miracle of biology that barely manages what it does. MRI studies of animals suggests that changes in senses would require a corresponding change in the brain to process the new information. Dogs have large chunks of their brain dedicated to processing smell and for a human to have an enhanced sense of smell, the brain would have to be re-ordered. Even controlling such things as a tail (allowing conscious control over its movement) or retractable claws would likely require neural re-engineering which is likely to either be very difficult, or even impossible.
Interior Transplants: Although this does not allow a physical transformation as most fans of transformation literature seem to prefer, it does allow interesting story ideas. More efficient organs could be genetically created and transplanted, allowing longer breathholding, better physical performance, or even seeming miracles. Different lungs could be transplanted to allow breathing of alternate atmospheres, such as a partially terraformed Mars. Alternately, plain organ transplants could extend life, suggesting a rush on organs for transplants. Organs could even be replaced with cybernetic devices allowing even further enhancements, such as stored air for hours (just hope nothing punctures the tank). It might even be possible to graft cybernetic storage devices onto the brain, allowing eidetic memory or implanted skills, knowledge, or even personalities. Individuals could have a permanently implanted cybernetic AI as a personal aid/confident to search the nets for information, to remind of schedules, to talk. Or to control the body from the outside making the biological brain a helpless prisoner.
A note on brain modification: We don't understand at this point, other than in the most general sense, how the brain works. We know how neurons work, but what is mind? What is self? What is sentience? One theory is that an individual develops by trial and error, trying various combinations like a neural net until skills are learned, such as communication. This would mean that my consciousness would think of something, that thought would be translated through a trial and error taught filter to a word which would then be spoke. Your physical body would hear the word, it would be pass through your trial and error taught filter until finally your consciousness interprets the information. Though studies have confirmed that common functionality seems to occur in the same gross areas of the brain from one individual to another, the specifics may be unique from one individual to another making any kind of direct neural interface different from individual to individual. In other words, it's not as easy as cyberpunk makes it out to be.
Brain Transplants: There is nothing theoretically unlikely about taking a brain, and transplanting it into a new body. And, as the body was genetically engineered and grown in a vat, it can be just about anything desired. The problems with this though are having the brain control features of the new body, particularly senses or limbs, and making sure that the brain could fit into the body. No normal sized raccoon transformations by this method. If the brain is better understood, it might be possible to restructure the brain as required for a new body, or one may be forced to grow neural clusters to control new features, allowing the actual brain only the grossest access to the new limbs. For example, a tail controlled in this manner would literally have a mind of its own. It might react to hormonal changes within the body (such as anger), or might continue oblivious to how the owner feels. It might also be difficult or impossible to link a brain to a new nervous system, which suggests that one might have to transplant the brain AND the nervous system. This could be done by suspending the body in a tank of nutrient fluid, and releasing a virus or nanomachines which consume everything EXCEPT nervous tissue and brain tissue. It could be possible, if nervous tissue could be grown, to transplant a brain into a new body, grow hard wired though untrained neural structures to control new limbs/senses, and have the brain consciousness learn to use the new equipment.
Remote Control: If a direct data link to a brain can be achieved, either by a surgical procedure, or by a slow creation of a unique interface through trial and error by nanomachines, it would be possible to remotely control a properly equipped host body via a kind of telepresence. One could be put into an isolation chamber, and have the sensory input of an appropriately wired creature such as an animal, or another sentient, sent to the isolated body. If both bodies are equipped, it might be possible for one body to give commands remotely to the other body, or possibly each could control the other body simultaneously (some kinky sex ideas here). Likely though the control would be somewhat limited, and likely the remote body would feel at least somewhat 'numb'. However, if enough bandwidth is available this could be overcome.
Virtual Bodies: An alternate method, if a direct neural link can be achieved bypassing the senses, would be for the host to control a virtual body within a virtual environment. Within such an environment, anything would be possible as long as the data stream could contain the information, including instantaneous transformation. However, the problem of extra limbs would still exist. They could be controlled by coded macros, but would be unlikely to be directly controlled by the host mind.
Mental Transference: A sufficiently advanced technology might be able to isolate the consciousness within a biological brain and copy it, either onto cybernetic hardware, or into another biological brain. As only the consciousness and memories would be copied, a new body could have wiring for new limbs/senses - assuming the existing consciousness could be mapped onto a new neural structure - and new limbs/senses could be controlled though their use would have to be either learned, or implanted through fake memories/knowledge created artificially. The one problem with this is that the brain is continually changing, and thus the brain would have to be frozen at one point for such a copy to be made. This could be done by a 'safe' freezing, or might require the individual to be killed, and then the brain sliced and copied before it begins to decay. And in this case, if something goes wrong, you are dead.
Retro Viruses: There has been a lot of talk about viruses written to infect cells and then rewrite the genetic code within the individual cell. At first glance, this suggests that it might be possible to actually have a body transform gradually over time, but the problem is that most tissue is either done growing very early, or doesn't grow any more. Bones would not change. This method could be used to modify soft tissue including such things as hair colour and skin colour, and could allow the growth of fur or possibly scales over the skin. But the actual shape would have to remain human.
Nanomachines: This is the other 'magical' technology that a lot of writers use. Nanomachines are devices that are equivalent in size to molecules that would be injected into a body and rebuild cells and organic structures to a new model. There are many problems with this, not the least being what happens to the heat generated, and why the person doesn't die as their body explodes in seemingly uncontrolled cancer. If the nanomachines modify the brain chemistry, then likely the individual would be destroyed, creating a new brain that could learn to be another person. In a very controlled fashion, limited physical changes could be done over time, as bones were lengthened, muscles lengthened, etc., but it would have to be done one step at a time and very carefully, and the head would still have to remain human sized to hold the brain.
Biogoo: It might be possible, if the brain is fully understood, to write a retro virus, or program nanomachines, to rebuild the body into a non-differentiated biology with a distributed neural processing network that is structured to recreate the individual brain. This 'biogoo' could shape itself into different forms by limited cell differentiation and allow actual transformations, though it is likely that a great deal of time would be required to change from one form to another. The individual would likely have to cocoon him/herself and spend weeks or months dissolving the old body and growing the new.
Genetic Engineering: Alert readers have probably realized that a lot of the problems listed above are derived from having to retain the individual during the transformation. There is nothing wrong with creating a new life form and letting it develop its own mind and consciousness, but this is not really a transformation of an individual, more a transformation of the race.
Doubtless I have missed methods, but hopefully there's a lot to think about here. Use it for ideas, but don't let it limit you.