The Neuroscience of Darkships

by Tedd Roberts

DarkshipRealistic descriptions and usage of science are hallmarks of Science Fiction. While "The Golden Age" of SF was often written by scientists, mathematicians, engineers, or those who worked intimately with science implementations and concepts, modern SF often struggles with realistic science. The portion of the genre termed "Space Opera" has remained true to a vision that the science is part of the story, even though it need not be the major focus. In general, SF readers tolerate a few gimmicks such as "Warp Drive," "Inertial Compensators" and "Autodocs," but the rest of the science needs to be believable based on current scientific knowledge. Sarah A. Hoyt's Darkship Renegades is most assuredly Space Opera--an epic quest, a sweeping scale, an intimate struggle between individuals, and sound--if speculative--science. The story development of "Hampson's Disease" in Darkship Renegades started quite simply: Sarah asked for a scientifically sound (if speculative) rationale for one individual to start having someone else's memories. Together we developed not just the mechanism for memory transfer, but also a disease to justify it, based on current knowledge of the human brain.

lost cells erase memory, skills, and personality

Figure 1: Diseases and head injury cause the death of "neurons," the basic information processing cells of the brain. Loss of these cells "erases" memory, skills, and even personality. Image copyright by Lightspring, 2012. Used under license from

Medical science is quite familiar with degenerative diseases of the brain and nervous system similar to, if not the same as, the disease Sarah and I created. Notable diseases of this type are Parkinson's, Alzheimer's and Huntington's Diseases, which cause breakdown in muscle control, cognition and memory due to death and degeneration of the essential cells – neurons – that support the information processing functions of the brain. Other diseases such as amyotrophic lateral sclerosis (ALS, "Lou Gehrig's Disease") and multiple sclerosis involve loss of the long neurons that connect muscle and sensory systems back to the brain.

Loss of neurons is an important mechanism in degenerative brain disease since it removes the cells that support the functions of cognition and memory, yet there is a more subtle feature that would leave the brain structurally intact while still losing essential function. Each neuron makes thousands of connections with other neurons, and it is these connections--"synapses"--that do the actual storage and processing functions of the brain. It is one reason why simply building a computer with the same number of processors as neurons in a human brain will still fall short of duplicating that brain's function. It would be necessary to build a computer with the same number of processors as synapses (at least three-to-four orders of magnitude higher than the number of neurons) to even come close to duplicating a functioning human brain since the connection strength, number and exact configuration of synapses are how memory is stored, skills are learned, and movements are correlated.

neurons connecting via synapses

Figure 2: Neurons connect via "synapses" in which electrical activity of the sending neuron (top) releases chemical neurotransmitters that initiate similar electrical activity in the receiving neuron (bottom). Image copyright by Alex Luengo, 2012. Used under license from

There are diseases currently known to twenty-first-century medical science that selectively attack synapses--Alzheimer's disease affects synapses and neuron cell bodies--but a more specific example is Myasthenia Gravis in which the body's own immune system attacks the synapse between muscle and the muscle control neurons (Motor Neurons). Many of these diseases are associated with age; it has been estimated that if humans lived long enough, we would all exhibit one or more of the degenerative diseases known to affect the human brain. Thus Sarah Hoyt is well within the bounds of speculative fiction to propose a disease that would be exhibited only at advanced age--greater than the current norm for human population, but well within the range of humans genetically engineered to avoid the most common medical diseases.

How then to treat such a disease? Modern medicine has had limited success with techniques to restore neurons or promote regrowth: with a few exceptions, we do not regrow brain cells--in fact humans are born with more brain cells than at any other time in their life! The process of maturation and growth requires the "pruning" of neurons and connections. Surgery does little good when the remaining cells cannot grow and fill in the missing areas (such as cut skin or a broken bone). So-called "cognitive enhancing" drugs may slow down the progress of the disease, but cannot repair the existing damage. In the 1980's and 1990's there was some hope that Parkinson's Disease could be treated by culturing and transplanting the neurons that produce the neurotransmitter chemical dopamine; thus providing a repair by virtue of replacing the dead or damaged neurons that cause the symptoms of the disease. In a similar manner, twenty-first century research has turned to stem cells--nonspecialized cells that can be programmed to develop into neurons--replacing populations of neurons lost to disease. However, while such replacement therapies may restore some function by restoring the baseline neural function, it cannot replace specific learned or remembered functions that rely on specific patterns of synapses connecting neurons. Thus a "cure" for advanced degenerative brain disease must include a restoration of synapse connections.

In Darkship Renegades, the Science Fiction answer to the question of restoring synapses is a form of nanotechnology – the Nanoscale Emitters / Nanoscale Assemblers or "Nessies." The NSE/NSAs are pure speculation at this part, but there are micrometer-sized machines in existence now, and smaller size ranges are certainly forthcoming. From a (joking) email:

Dear Professor Hoyt:

Thank you for your inquiry regarding our medical nanoscale emitter / nanoscale assembler prophylactic treatment options.

As you know, the NSE / NSA represents a revolutionary method for medical neuron repair and restoration of function following debilitating neural diseases.  An outgrowth of our deep scanning project at the Inverness Research Station in collaboration with the University of Glasgow, the nanoscale devices in "emitter" mode are administered via transnasal delivery to ensure that the NSEs pass the blood-brain barrier and enter the cerebrospinal fluid.  Once in the CSF, the NSEs self-organize into a scanning network to analyze and map neurons and neural connections.  Communication between NSEs utilizes femtometer wavelength NIXINET communication to pass neuron configuration information from device to device, resulting in a shared database of all neuron connections. 

As long as the CSF does not contain proteins indicative of neuronal damage (i.e. Tau, amyloid, presinilin, heat-shock protein 90, etc.) the NSE network remains in update mode, continuing to map new connections consistent with learning and memory, and storing the revised "healthy" neural connectivity map in the distributed molecular memory of the NSEs.  Upon detection of neuronal damage, the NSEs convert to nanoscale assembler (NSA) mode.  Once activated, the NSAs provide two key functions leading to neural rehabilitation.  First, NSAs provide trophic and metabolic support to promote stem cell proliferation and replacement of damaged neurons, glia and microvascular components.  Second, the NSAs actively restore neuronal connections (via insertion of synapsin and receptor proteins) in the form of patterned synapses specified by the neural configuration data stored in NSE mode. 

Initial studies have been promising, yielding 99% restoration of neural function with complete memory retention.  The NSE/NSA method is effective in preventing debilitating effects of head injury, stroke, and 116 known neurodegenerative diseases.  We have also determined a 75% success rate in reversing neural damage even without prophylactic NSE treatment.

If I may be of any further assistance, please do not hesitate to contact me,

Warmest regards,

Prof. Hampson, Institute of Medical Science, University of Aberdeen

Yes, it was meant to be humorous. Use of the "redshirt" name and the veiled reference to Loch Ness were an inside joke during development of the backstory. Still, the email provided the basis of the next issue encountered when creating both the disease and the cure: Given a means to restore synaptic connections, what pattern should be restored? Obviously to restore a patient of degenerative disease, the pattern should be of the own patient's healthy brain before (or shortly after) the onset of the disease. But what if we were to try imprinting a different pattern? Cloned humans, as introduced in Darkship Thieves, are essentially blank slates--a fresh brain with the genetic tendencies, but none of the memories, skills or personality of the original. Certainly the clone can be raised normally from child to adult, but the memories, skills and experiences of the clone can never match that of the original. However, if all (or a majority) of the synapses in the brain could be restored to the original's own pattern would it be the same original? In theory, yes. Given the same genetic structure, duplication of the complete pattern of synapses could very well produce an exact copy. This could be a problem in that there is now a doppelganger that looks upon the original as an imposter, a stranger that is not "myself." For the viewpoint of the original, they do not get to live on in a new body, and will eventually die. Only the duplicate will have the experience of life extension.

patterns and connections between neurons and synapses

Figure 3: The unique pattern and connection strength of synapses between neurons forms the basis for memory, learning and even personality. Image copyright by Lightspring, 2012. Used under license from

It is the intermediate process that is largely unknown: Will both individual personalities "share" the mind, brain and body until the duplication process is complete? Clearly a complete restoration of synapses will replace the connections that constitute the "native" pattern and the brain will become totally that of the imprinted pattern. However, the incomplete transformation could very easily produce a mix of memories and personality, similar to that of multiple personality disease. Consider first, that memory patterns are (a) distributed throughout large areas of brain, and (b) robust enough to reconstruct whole memories from only fragments of recollection. Thus, it is quite possible that unless the imprinting is instantaneous, there will be a period of time during which the brain will contain portions of both patterns. Then, too, are studies of individuals with multiple personality disorder which demonstrate that EEG and patterns of brain activity are different for the two (or more) personalities exhibited by a patient. Under these circumstances, an incomplete synaptic restoration may indeed look very much like multiple personality. So as not to create too many spoilers, I will say no more at this point. For more on how these ideas play out in the book, you will just have to read it!


A final note on the plausibility of the science in Space Opera in general, and in Darkship Renegades in particular, is the genetics of the "Mules." Sarah--particularly through her characters Athena Hera Sinistra and Doc Bartolomeu--maintain that the Mules are not human and cannot interbreed. One might reasonably ask how a derivation from the human genome would not still be human. There are a number of logical changes to the human genome that could render it incompatible with unmodified humans. First is that the normal mechanisms of genetic drift and speciation are subtle. Small changes in genes in two isolated populations may occur at the same point on one of the 23 pairs of human chromosomes. Each offspring receives one chromosome of each pair from each parent. The actual genetic outcome is a combination of the genes received from each parent, yet if those genes are incompatible, they are at best nonfunctional, and at worst, detrimental to survival (such as the recessive gene for hemophilia). Continued genetic drift leads to incompatibility for breeding and the formation of separate species. The "Mules" of Darkship Thieves were specifically genetically engineered, and again without revealing too much of the plot, we learn in Darkship Renegades that there were many different genetic engineering designs produced by different countries and companies, and for different purposes. This is speciation and genetic drift writ large, on a canvas the size of Earth. The human genome is complex enough that totally different sites on our 46 chromosomes could be manipulated for similar outcomes, while still maintaining incompatibility between the genetics of any two (or three or four) Mules.

A second type of incompatibility would logically be addition or deletion of a chromosome. It is unlikely that humans can achieve this via current medical technology, however, this is Science Fiction, and thus not beyond the realm of possibility. In fact, it occurs in Nature all the time. The consequences of inappropriate chromosome pairings are obvious even at our current level of medical knowledge. "Trisomy," the presence of three instead of two chromosome copies, of Chromosome #21 leads to Down syndrome. Mismatch of the XY sex chromosomes (#23) leads to ambiguous gender issues and sterility. Trisomy of Chromosome 13 leads to heart, brain and kidney defects as well as polydactyly – addition fingers and toes. At Chromosome 18, trisomy also leads to organ malformation and webbing or fusion of limbs and digits. Such instances are rare, and the truth is that trisomy of chromosomes. The plain truth is that trisomy is generally fatal, except in rare cases and the known Chromosome 21 and 23 syndromes. The reverse--monosomy, a single chromosome instead of a pair--is not viable at all except for Chromosome 23. A human female with a single X chromosome, known as Turner syndrome, is indeed viable, but sterile and with shortened lifespan.

Thus manipulation of either the specific gene sequence or the number of chromosomes would certainly serve to keep the Mules from interbreeding with humans. As long as all of the Mules were male, they could not reproduce with normal human females; a female Mule would be necessary for breeding. In Darkship Thieves we learned that female was 'Thena; however, she would have to have been very carefully genetically engineered to be compatible with more than just her "parent" if she was to be the mother of a new race of Good Men of Earth.

Thus the Science in Science Fiction is an important part of story and plot. It must be realistic, containing enough modern or known science, with speculation right at the edge of what we know. Sarah Hoyt has done a masterful job of blending a compelling Space Opera with a classic approach to science worthy of the name. Technology and science advanced to the point that it is indistinguishable from magic has its place, but the result is so much more akin to Fantasy. It is refreshing to read Darkship Thieves and Darkship Renegades, for the stories of course, but also for the Science Fiction.

Copyright © 2012 by Tedd Roberts