Issue 194 – November 2022


The Neuroscience of “Babirusa”

Human minds are fascinating machines. They are able to process photons, soundwaves, and various other physical phenomena, turning the information into thought, emotion, and cognition—experience. They take snapshots and store these experiences to reemerge as memories in the presence of a reminder, then use those memories to generate fantastical simulations during dreams—experiences in their own right. As humans, we can convert complex, abstract concepts into generative language that has infinite possibilities, because it is communicative, structured, dynamic, and symbolic. This ability to communicate leads to complex networks of society, laws, and ways to judge morality. We, as machines, are perfectly crafted to observe and interrogate the nature of reality. It was inevitable that we turned that inclination inwards, through neuroscience, to try and decipher ourselves.

In my novella “Babirusa,” I wove in various themes of interest that neuroscientists are discussing and tackling, at the systems and computational levels as well as through direct perturbations by synthetic biology. In particular, I focused on reality, personality, and morality. Of course, since “Babirusa” is science fiction and not real, there was some hand-waving in my speculative science inventions.

Still, the hypotheses and technologies I came up with are rooted in real science, which is worth discussing.

What Is Reality?

Several characters in “Babirusa” inhabit a reality very different from the one around us. They move through a maze of staircases and chambers dictated by an eight-dimensional number system. In this world, painted objects in one painting can move to another, faces are blurred, music sounds without a source, and various other laws of physics seem to be breached. An important question in the story is whether their reality is just as valid as the one we are all used to.

The question of “What is reality” is not one that has a singular answer. One way to define it is through our physical universe, dictated by limitations of special relativity. Here, we all trudge along our world lines, the paths we trace through space-time, made of “events.” Unless the geodesic of space-time is warped to a curvature high enough for these world lines to circle back in on themselves—which is unlikely—we will not be able to physically revisit events from our past, and our arrow of time will flow with the unchangeable increase of entropy. This physical world is also what generates the photons, sound waves, odorants, and tastants. All of these interact with our sensory organs to ultimately send signals through that massive tangle of computation that rests in our skulls, allowing us, in this definition, to perceive reality.

What if we define reality in the opposite way, though? Reality isn’t the world around us, but how our brains interpret it. Those photons and sound waves could all disappear, and we would still see and hear things if neurons fired in our visual cortex and auditory cortex. We can even travel back in time when we define reality this way. All of the activity in our sensory cortices is being monitored constantly by a part of our brains called the hippocampus, which receives projections from neurons everywhere in the brain.

If the hippocampus gets a signal that a portion of experience is notable, it captures it by associating a small, recurrently connected, unique group of neurons with that snapshot of experience. An engram. In the presence of even a portion of the sensory information associated with that experience, also known as a reminder, the entire hippocampal engram will fire. Through a circuit that works very much like an encryption algorithm responding to a key, this event will cause all of the areas of the brain that were active during the original experience to reactivate. Bringing back a lost moment in time to the present, as a memory.

The memories that are chosen to be kept long term get transferred out of the short-term storage site in the hippocampus through slow-wave sleep, in a process called consolidation, to integrate with other patterns of brain activity. The integration takes place during REM (rapid eye movement) sleep, a time of fantastical simulations and mind-bending realities—dreams. Can we consider dreams valid experiences? We have memories of dreams, after all. Possibly even memories of dreams that are chosen for long-term storage and integrated again as part of a new dream—a jumbling of a jumbling of experience. But we can also run, walk, even fly in dreamworlds, break any rule of special relativity we want, all while a serotonin projection to our brainstem locks our physical bodies into a temporary paralysis.

Perhaps the definition of reality lies somewhere in between the world we generate and the world we receive, within the spread of how far our perception can warp from the concrete world line we follow. We still are people, in our dreams, even if those characters live a wholly different life from ours, or aren’t “us” as we would be in our awake moments. We emote, think, and logic our way through situations, just as we would in our awake realities. Are those dream characters valid humans? That brings us to the next question.

What Is a Personality?

In the story, five characters occupy the space of a single brain. Four were once components of the fifth (a young woman named Roop), but were removed and locked away, an event that created them as full people and permanently altered the personality of Roop.

Our identities are each unique as a fingerprint, the product of our specific autobiographical timelines. Our memories feed into our decision making in a constantly updating subconscious stream, as do our current environments and experiences, which we wouldn’t have found ourselves in without our chain of past decisions. In computational models of conscious and subconscious decision making, these factors of memory and current environment can be turned into a probability distribution. This comprises of a spread of likelihoods that different decisions will be made by an agent in a given environment, and can give us insight into what the most probable decision will be.

That “most probable decision” and the spread of other likelihoods around it—could that be one definition of what a personality is? After all, the spread of likelihoods takes into account the entire history of the agent, and makes a prediction of what its decisions will be. Those decisions could be seen as both the creators and the embodiments of personality.

So, if you hide a portion of that memory bank away, preventing it from contributing to this prediction of what decision to make, that spread of likelihoods will also change. The “most probable decision” will no longer be the same. And if the sort of choice you are most inclined towards changes, haven’t you yourself changed?

The act of making a decision will not go away, no matter what you eat away at within the memory bank or environment. And if that is where a personality lies, then it does not matter how many memories are contributing to that decision, or what those memories are, in order for a personality to exist. All that matters is that the spread of likelihoods of decisions will be generated.

So, in “Babirusa”, when those components of Roop’s memory bank are removed and put into a separate system still running parallel to her consciousness, they are still feeding into the same mathematical operations that Roop’s consciousness is feeding into. They might consist of fewer memories, sure, but that is not what matters—they are converted into agents, put into situations, and are tasked with making decisions. Even though their spread of potential choices will look different from the original Roop’s, and are generated from fewer memories, couldn’t they be equally valid as consciousnesses and personalities?

Our decision-chains, combined with our ability to communicate with and observe the decision-chains of others, lead to intricate webs of judgment and universal guiding principles for what sorts of choice-inclinations, or personalities, we should strive to have. Our brains are all ultimately driven by sugar and shocks, rewarding and aversive stimuli, and humans self-organize into civilizations, which are simply vast systems of human brains. What personalities will lead to a life of more sugar, and what personalities will lead to a life of more shocks, are dictated by this organizational structure, which can be looked at through another fascinating neuroscientific lens.

What Is Morality?

The core theme of “Babirusa” is morality. Morality can be looked at from many perspectives, and, like reality, is not easily defined. An action’s judgment as “morally good” or “morally bad” can change when viewed at global versus local scales, when information about the decision-chain leading up to the action is hidden or not hidden, or if the judgment of the action is taken from an egocentric versus allocentric point of view with respect to the agent taking the action. The story attempts to discuss as many scales and perspectives of morality as possible through the characters’ decisions and the world they inhabit.

We are very inclined to attribute moral value to everything in the world around us. In tasks where we watch simple shapes interact on a screen, we instinctively assign the shapes intention and moral value. Researchers at Harvard and MIT even created a computational model called the Moral Dynamics Model that can replicate this phenomenon, quantifying characteristics of a situation that contribute to our judgment based on things like distance a shape travels and duration of its contact with other shapes, which influence how we infer effort exerted and consequently our assignment of “good or bad” to a shape (Sosa et al. 2021).

Modeling morality in this way could prove very useful in the future. If we understand the factors contributing to how we define something or someone as good or bad, we can begin to view methods of organizing society with a more quantitative and objective foundation. We might be able to see where things go wrong in our global-scale systems, and how to work towards solving issues like pervasive systemic biases and unfair criminal justice policies.

Engineering Brains

Synthetic biology is the field of engineering organisms to change their abilities or to give them new ones. An example of this is optogenetics, where a light-sensitive ion channel protein is inserted into a neuron’s cell membrane. This allows for a fiber-optic cable to shine a light onto that neuron, which will open the channel and allow positive ions to flow into the cell, making it fire an action potential. Another example is calcium imaging. An action potential in a neuron results in calcium channels opening at the neuron’s synaptic terminals, flooding the cell with calcium that ultimately leads to release of neurotransmitters. By adding a synthetic protein that fluoresces when it binds to calcium, we can use a microscope to image these events of calcium flooding and neural activity as they occur.

In “Babirusa,” the speculative synthetic biology (called Babirusa) was used to identify the threads of instincts, memories, and emotional maps in Roop that led her to commit a crime, and then prevent those instincts, memories, and emotional maps from ever influencing her again, by storing them away in a parallel system within her brain and referring to that parallel system to specifically inhibit them if the associated neural activity ever began to appear.

To design this, I thought through the cell biology of a neuron. Dendrites of a neuron have channel receptors for the neurotransmitter glutamate. If glutamate binds to these receptors, the channel opens and positive sodium ions flow into the cell. Once enough sodium flows in to reach a threshold voltage, voltage-sensitive sodium channels also open and this causes a flood of sodium into the cell, called an action potential. Once another voltage threshold is reached, voltage-sensitive potassium channels open and potassium ions flood out of the cell. This brings down the charge again and after a short refractory period, the cell would be ready to fire another action potential.

The action potential propagates along the axon, which is wrapped in a sheath called myelin. Myelin allows the signal to travel very quickly. At the end of the axon is the synaptic terminal, where the action potential opens voltage-sensitive calcium channels, and calcium ions bind to vesicles full of neurotransmitters, driving them to the membrane, where they release their neurotransmitter out of the cell.

In the Babirusa, “RecorderBots start out as a blank template and embed themselves in neuron membranes. They send their neural recordings and activity data to the AxonBots, which are embedded within the insulating myelin sheath surrounding the neurons’ axonal projections. The AxonBots run parallel to the true neurons’ axons, without touching them, and are wrapped in a special type of lipid protective layer. They are able to transmit electrical signals to one another at incredibly high speeds, immune to degradation because of their highly conductive graphene lattice structure, and create pathways that all lead to a central nanobot assembly, the Beacon.”

Since I needed a way for my character Kabir to try and stop the Babirusa, I had to consider materials that would have a weakness. I chose stacked graphene lattices for the AxonBots. Graphene is made of a hexagonal lattice of carbon atoms. When researchers stacked graphene sheets on top of one another into a superlattice, and rotated two graphene sheets at an angle of 1.1 degrees, the superlattice turned into a Mott insulator, not letting current flow through despite having an electrically conductive structure (Cao et al. 2018).

If a material’s atoms’ last energy band is filled with electrons, it is considered an insulator, while if the last energy band is only partially filled, it is considered a conductor. Mott insulators have energy band structures that seem like they should be able to conduct electricity, but have an interesting property where because of electron repulsion, the half-filled energy band splits into two bands and keeps one of these halves empty and the other entirely full. This is what blocks electrical current from flowing.

This ability to switch between conductor and insulator was ideal for my story, as Kabir was able to figure out a way to stop the Babirusa by designing a synthetic protein that would rotate the graphene lattices 1.1 degrees and turn the AxonBots from conductive to insulating. The rotating protein he used is a real protein called dynamin-GTPase, which wraps around necks of cellular vesicles as they form at a cell membrane to pinch them off. As he says in the story, “Once this rotation is complete, the AxonBots won’t be able to communicate with the Beacon, and the Beacon won’t be able to communicate with the AxonBots.”

I hope “Babirusa” helps introduce more people to the creativity that science thrives on, and to the fascinating questions neuroscience can address about the nature of ourselves and the reality we inhabit. Science fiction is just that—a wonderful tool we can use to celebrate science and a condensation of the process of research. We can lay out hypotheses, design experiments, and even do something that’s unique to stories: explore the human impacts of what we do to an unparalleled degree.


Cao, Y., Fatemi, V., Demir, A. et al. Correlated insulator behaviour at half-filling in magic-angle graphene superlattices. Nature 556, 80–84 (2018).

Sosa, F.A., Ullman, T., Gershman, S., Tenenbaum, J.B., & Gerstenberg, T. Moral Dynamics: Grounding moral judgment in intuitive physics and intuitive psychology. Cognition (2021).

Author profile

Arula Ratnakar is a neuroscientist, science fiction author, and artist. Her four published stories can be found in Clarkesworld Magazine.

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