Do We Have A Soul?
I’ve encountered a number of atheists asking if there are those among us who believe in “ghosts” or “souls.” As you may know, I not only do *not* believe in any God or gods, but I also assert the reality of the physical universe and our ability to understand it by asking it about itself, i.e. by doing experiments or tests. That’s why I call myself an “empirical physicalist.”
In my novel “The Reality Thief” Darian Leigh, at a welcoming lunch on his first day in his new job as Assistant Professor, has a discussion about whether or not there is a thing as the human soul. I’m going to let Darian carry it from here. I ended the argument rather abruptly in the novel for plot purposes, so I’ll be back with my take at the end.
* * *

They ordered and ate their meals, confining their remarks to trivial appreciation of the food and scenery, and were relaxing over coffees and teas when the conversation took an unexpected turn. “I was sorry to hear of your father’s death this past winter,” President Sakira offered, “I’m sure he is in a better place now.”
“I doubt that he would prefer an urn over our house in California,” Darian responded.
“I mean,” the University President corrected, “his soul in heaven.”
“Of course,” Darian said. “His soul. Well, I’m quite sure that, prior to his death, my father was finally convinced there is neither heaven nor hell, and that the whole concept of souls is simply a reflection of a very human inability to accept that our brief physical existence on this planet is really all there is. He accepted his death as his ultimate end.”
Dr. Pratt could not resist weighing in. “That couldn’t have been very comforting to him.”
“I’m sure it wasn’t as comforting as his previous belief in the myth of an eternal afterlife. After facing the prospect of his imminent death for two years, my father was finally able to accept that nothing that was uniquely him would survive the cessation of coordinated biological activity in his brain. We had many discussions about this during his battle with cancer. I think he was brave to discard his earlier superstitions and face his death without emotional crutch.”

“I hate to say it, Dr. Leigh, but you sound rather heartless,” Dr. Pratt retorted. “Science has little if anything to say about the existence of a soul or spirit, if you will, nor about the possible existence of heaven.”

“That is not at all correct.” Darian’s three post-docs gasped in unison. Pratt was an internationally respected moral philosopher whose moderate religious views were perceived as generously inclusive.
“I would be interested to hear how you believe the study of natural law can contribute to our understanding of the transcendent,” said Pratt.
“Very well,” agreed Darian. Kathy rolled her eyes discreetly. “First, I need to know which version of the soul you might subscribe to.”
“Version?”
“Yes. Do you believe the soul is just a kind of energy that temporarily occupies the brain or body and is returned to the universe upon corporeal death, where it simply dissipates? Or do you believe that the soul is an organized structure unique to each person? That it can think or feel, and possibly, remember? The soul alluded to by most religions would generally belong to this latter category, I think.”
“If those are my alternatives, I will go with choice number two, that the soul is eternal and unique to each person. But I reserve the right to revisit choice number one.”
“Fine. Can you accept the compendium of sub-atomic particles that constitutes the Standard Model of Physics, as incomplete as it may be?”
“Certainly.” Dr. Pratt was reasonably well-versed in modern physics, considering it to be a sub-interest of sorts to reconcile common scientific and religious viewpoints. “But, the soul belongs to the supernatural.”
“And what exactly is the supernatural?” asked Darian.
“Something outside the laws of nature,” Pratt replied by rote.
“But a supernatural soul would still need to interact with biological matter, no? With cells made of molecules, those molecules consisting of atoms, those atoms formed from the various sub-atomic particles, all behaving according to the laws of nature?”
“Of course.”
“How exactly would it do that?”
“I don’t know. It’s supernatural.”

Darian’s entire body bobbed eagerly. “Mm. This is the crux of the problem. The known particles of physics interact with each other in well-understood ways. For example, electromagnetic forces are carried by photons passing between particles such as electrons—”
“Well, you and Dr. Wong are the experts on the various particles and forces. But, yes, that is also my understanding.”
“And a supernatural soul—if it doesn’t interact with the brain in any conventional manner—would still need some kind of mechanism to exchange information with the normal matter of the brain in order to affect the body’s actions.”
“I agree.”
“So, if we were to speculate that a soul is some sort of, as yet undiscovered, force, we would still have to admit that it can somehow interact with the normal matter of our brain, no? Otherwise, both body and soul would exist but would have no relationship to each other.”
Dr. Pratt chewed on the idea. “Well, there is certainly some kind of interaction. Our life experiences and the moral judgements we make on Earth must be reflected in our soul. If not, how could we be judged fit for Heaven?
“So, if the soul is some kind of matter or energy we haven’t yet discovered and it interacts with normal matter, it must do so through some force or particle we also haven’t discovered yet.”
“I would certainly agree that we haven’t found any ‘soul particle’ yet.”
“So one important question is: how does the soul know the matter it’s associated with belongs to the brain of a human, and not to a chimpanzee or a dog, or a fly? After all, biologically, neural cells from many different species are largely indistinguishable.”
“Certainly there are some differences between the cells of a man and those of a fly,” said Pratt.
“Of course, there are. But would that require the soul to read the DNA of the cell? Or would it just recognize cell-surface proteins the way another human cell would?”
“Let’s say the soul recognizes human DNA.”

“Okay. Given that chimpanzee DNA is about 98% identical to human DNA, do chimps also have souls?”
“I think that’s a trick question.”
Darian laughed. “Good for you. It is a trick question. You know that the DNA between male humans and male chimps is more alike than between male and female humans.”
Dr. Sakira couldn’t help herself, “That explains so much.”
Pratt smiled indulgently. “While animals may have spirits of their own, only human souls are generally considered to be made in God’s image. So, let’s say the souls we are discussing are uniquely human.”
Darian became serious again. “Okay. Let’s specify that the soul can recognize some subset of the DNA present in male and female humans that is uniquely human. Unless you would like to deny that human females have souls?”
Dr. Pratt looked at President Sakira and Kathy. “I think I had best not deny that,” he said with a wry smile. Sakira returned the smile graciously.
“Okay, so the soul recognizes some unique human brain DNA. Do you see the problem here?”
“Yes, I think so. Since the DNA of all the cells in one person is essentially identical, it would need to be able to specify some non-DNA recognition mechanism that is specific to the brain, wouldn’t it?”
Darian smiled. “Exactly. Now, we still could allow the soul to recognize some surface molecule encoded by the DNA but only expressed in the brain.”
“Very well,” Pratt replied, “Let’s do that, although I’m sure you’ll find some way to make me regret conceding the point.”
Dr. Pinto, who had remained relatively quiet through lunch, chimed in. “Why can’t we say the soul somehow recognizes electrical activity in the brain?”
“Sure,” said Darian. “I imagine we could make a case that there is some pattern of brain activity that is uniquely human, perhaps even unique to each human. And perhaps that would allow the soul to stay attached to the body so long as the brain continued to be active.”
“I could accept that,” said Pratt.
“That would obviate the question of how a soul knows its host body is dead. If it just recognized molecules instead of activity, one would think it would stay attached after death until decomposition was complete.”
“I hadn’t realized the discussion was going to become so morbid.”

“My apologies,” Darian briefly bowed his head in mock contrition. “However, even this would still require the so-called soul particles to interact with active neurons, with their molecules and atoms. We already have a model for how that might work, if we take a look at the dendy lattices. The semiconductor dendy sensors position themselves at synaptic junctions in the brain so they can detect and modify the neurochemical activity. One reasonable place to look for the soul-brain interface would be at those synapses. I see two possible ways it could do this.”
“Only two?”
“Logically, that’s all that’s possible. First, there could be interactions that we haven’t discovered between the molecules in these synaptic junctions and the supernatural particles of the soul. Of course, those interactions would still have to act according to some sort of governing laws. Technically, that would make them supra-natural, not super-natural. Just because we haven’t discovered or explained these particles and interactions, doesn’t make them outside of nature. They would still fall under the purview of physics eventually.”
“But the supernatural is unknown and unknowable,” Pratt objected.
“Exactly,” replied Darian. “Accepting the possibility of such a mechanism would suggest that there are simply gaps in our understanding. We can surmise that we could eventually discover these soul particles and delineate their interactions with other particles.
“Perhaps we need to put a live human in a particle accelerator,” Pratt suggested.
“The fact we have never seen such particles suggests we might need to do something like that,” said Darian. Even Greg wasn’t sure he was being serious. “Of course, over time, the discovery of such soul particles could conceivably lead to the development of a technology that might include soul detectors, perhaps even soul modifiers or soul destroyers.”
“I don’t think I’d like to see a technology of the soul.” interjected Dr. Sakira.
“Me neither,” replied Darian. “If atomic soul particles actually existed, they could be horribly abused. However, Dr. Pratt also said that the supernatural is unknowable so that only leaves us with the second mechanism.”
“And what is that?”
“The soul interacts with the brain directly by altering the local natural laws for a short while. This is the very definition of supernatural. For example, the soul could alter the natural laws of physics locally causing an ion channel in a synapse to open and initiating neural activity. Souls could be composed of what one could call collections or fields of natural laws. But no science of any such thing exists; we have no understanding of how such fields might interact with each other.”
“In that case, souls would exist outside the universe of natural law. So science would have nothing to say about them, would it?” Pratt concluded triumphantly.
“Yes. In that case, souls would be outside the natural laws of this universe.”
* * *
Paul back. In the novel, I stopped the discussion here because it led Darian off on an inspirational tangent. That tangent eventually allowed him to develop the Reality Assertion Field, central to the series. The point of the debate here was to challenge the actual basis for the soul. What could it be made of? How could it interact with real matter in the universe? Clearly there are problems with conventional magical thinking about how that might work.
In a similar vein, one could even ask, “How does a soul think, or feel, or remember?” The definition of a soul as “energy” is unsatisfying because we know a lot about energy and it doesn’t seem to meet the requirements for soul. Energy transfers between particles, mediated by other particles. When the particles of matter that we use to store and manipulate energy, release energy into the environment, it dissipates. That raises the question of how energy could maintain pattern after the disruption of the matter that imposes that pattern, i.e. the brain, following death.
There are two beliefs about “spirit”: some think it’s a form of energy that is spread throughout the universe after death, and some believe it’s eternal and maintains pattern. The first definition is kind of meaningless to me as it’s indistinguishable from the physical disruption of the brain at death. Without the presence of mind emerging from the conceptual pattern making of the brain, there is no “person” to talk about after death.
People who believe the second thing: that the soul is eternal and maintains its pattern (memories, knowledge, beliefs, and personality) independent of the brain; are another thing entirely. Darian’s argument makes a strong case that nothing we have discovered could suit as the basis for building such a thing as a soul. So, why do people think there might even be such a thing? I mean, apart from wishful thinking that some part of us persists after death.

I believe this comes from our inability (so far) to understand the nature of cognition and of consciousness. Because we don’t understand how our thinking, our feeling, our experiences could all be emergent properties of a physical (and physiological) brain, we invent the “soul” to explain them. Of course, we have models for cognition; they’re called computers. They’re not good models but they suggest that it’s possible to build devices that have emergent properties not contained in any of their individual elements.
The program for playing chess in a computer is not built up from individual components of hardware or software, each of which knows how to play chess a little (equivalent to the consciousness elements of Qualia proposed by some). Instead, the ability to play chess is an emergent property of lots of lines of code and some data, interpreted as instructions by hardware. That’s a model (a very simple model) for cognition in the brain.
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Canadian author Paul Anlee writes provocative, epic sci-fi in the style of Asimov, Heinlein, Asher, and Reynolds, stories that challenge our assumptions and stretch our imagination. Literary, fact-based, and fast-paced, the Deplosion series explores themes in philosophy, politics, religion, economics, AI, VR, nanotech, synbio, quantum reality, and beyond.
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This one is ultimate answer as said: convinced there is neither heaven nor hell, and that the whole concept of souls is simply a reflection of a very human inability to accept that our brief physical existence on this planet is really all there is. He accepted his death as his ultimate end.”(fr the paragraph above) I don’t understand as why people gets so confused?
Hi I really enjoyed reading this. I understand why you found the first definition you gave of a soul as irrelevant since in this discussion the soul is seen as something unique to each person which differentiates them. However, I personally believe that the first definition given can make sense and be beneficial.
A common way the first argument is presented is that all living things are empty vessels which are filled from the same ocean, the ocean representing some type of energy or life force. In this argument the soul does not differentiate people but ties all living things with a common thread. This is beneficial because without this common thread we are just systems of sensory inputs and and outputs, however the soul provides us something innately good.
I know this is an old article but if you would care to elaborate on the first definition of the soul I would like to hear that as well.
Hi Nader,
I think the first definition you are alluding to is in the paragraph where Darian says, “Do you believe the soul is just a kind of energy that temporarily occupies the brain or body and is returned to the universe upon corporeal death, where it simply dissipates?”
The second definition (the one most commonly used by believers and the spiritual people) is in the next sentence, “Or do you believe that the soul is an organized structure unique to each person? That it can think or feel, and possibly, remember? The soul alluded to by most religions would generally belong to this latter category, I think.”
It seems to me that the first definition most closely resembles the kind of “energy or life force” you refer to where “the soul does not differentiate people but ties all living things with a common thread” where as the latter is more like the Abrahamic (or Hindu/Buddhist, for that matter) “soul” of many religions. Most of the argument presented is against the type of individual soul discussed in these religions.
I’ve discussed the kind of “energy or life force” in other articles on my paulanlee.com blog page. Briefly, as a molecular biologist, the idea that life requires some kind of “life force” is just absurd to me. Life is what we call the complex chemical system with all its various reactions and interrelationships; the idea of a “life force” or “vital spirit” holds no place in the modern science of living organisms. J. Craig Venter’s group has successfully converted one simple kind of bacterium to a different species by switching out its entire genome (all the DNA) for a chemically synthesized genome from another species, showing that the identity of a living organism is the direct result of its DNA. Biochemists understand a lot about the chemistry of life and no “life force” or “vital spirit” has ever been required to explain the reactions we observe.
If there is no “life force” or “vital spirit” then the notion of a common well or “same ocean” which invigorates life is simply not required. I concede that all life is connected by the chemicals we share (e.g. carbohydrates animals get from eating plants, shared gases, water, etc.) but there is nothing mystical or supernatural in that connection. Also, while I may share inhaled and exhaled gases with nearby plants and animals, my connection to organisms on the other side of the planet is remote, at best. Nearby connections are strong, distant ones are so weak as to be insignificant.
Along with this perspective, I thereby reject notions of the “love” force that interconnects us all. While we all share the physical forces of shared gravity, shared sunlight, and shared molecular, atomic, and subatomic forces (that is to say, we have a common set of physical forces) nothing should be read into that. It is like all chess players play by the same rules, but that doesn’t make me a grandmaster.
I see nothing bad about being “just systems of sensory inputs and and outputs”. I think this is somehow meant to be demeaning like saying “life can’t just come from inert, dead matter”. But complex relationships and interesting emergent phenomenon can arise from relatively simple beginnings. Complex proteins and DNA are assemblies of atoms whose properties inside a living organism aren’t easily predictable from an understanding of atoms and how they form molecular bonds. This is like trying to understand the behavior of a complex computer program by understanding the syntax of assembly language; it’s impossible.
So (no surprise) as a physicalist, I reject the mystical notions of a “shared ocean” of “energy or life force” that connects all living things. Within that, I also reject the representation of this “shared ocean” as being some kind of common soul we all share. It makes no sense, and is not at all required to understand life nor cognition/sapience.
I hope that helps, but please feel free to comment back if I’ve missed something or misunderstood your point.
Thanks – Paul
Thank you for your reply, you have understood my comment and I appreciate your insight. I look forward to reading more from your blog.
Just to clarify, I don’t mean “systems of sensory inputs and and outputs” to be demeaning I think that is the most simple and logical explanation of what I am. However throughout history people have craved mysticism and such an answer as above proves very unsatisfactory to meet their desires.
As a result the first definition could be seen as a more reasonable alternative to organized religions and in fact it is becoming more popular with new age spirituality. I also believe the first definition to be an atheistic definition along the lines of “God is Everything” in which god is a commonplace phenomena of the world not a supernatural force.
Sorry If I am delving too much into beliefs without concrete evidence but do you think for Atheism as a belief to gain more traction it would need to appeal to peoples desires of mysticism?
Glad I understood what you were saying.
My BSc was in computing science and I was particularly interested in cognitive computing and AI. I would add to your “systems of sensory inputs and and outputs” that we also have algorithms and data structures for converting those inputs into outputs.
I certainly hope atheism as a belief system (if it can be said to be so – many think not, which is why I call myself an empirical physicalist). Mysticism is antithetical to evidence and reason (which I would say form the basis for lacking a belief in God or gods). As soon as we accept (without evidence) any claims of mysticism, we are on the wrong path. On my paulanlee.com blog, I discuss people in the relatively new “spiritual but not religious” category. I always say, if you think everything is God, well, that’s okay. But we already have a word for everything: the universe or the cosmos. Why assign this other word the same meaning? Especially when most who believe in a “God” seem to want to embody that being in some kind of personhood. That is, I know of no existing religion that does not endow “God” with consciousness, intelligence, and intention (will). Clearly, the universe has neither consciousness, intelligence, nor intention (at least it’s clear to me).
There are a few reasons why I doubt atheism will ever gain the widespread traction of religious belief systems:
1) Religion is an embedded power. Believers will resist the idea that they don’t have the right to indoctrinate their children into their belief system.
2) Refuting religious beliefs is very difficult. Any system that demands its followers “double down” on their faith when they face a challenge to it has an almost insurmountable barrier to convincing. Many (but not all) atheists think that we should encourage more of a scientific (or at least physicalist) understanding of the universe. At a minimum, this would need an understanding of a) physics and cosmology adequate to support inflationary Big Bang models of the start of the universe, b) an understanding of evolution adequate to defend against intelligent design claims, c) an understanding of cognitive psychology/computing adequate to refute ideas of the “soul”. Few people have an adequate understanding to refute religious claims let alone support scientific claims. Science is hard and we’re mostly not up to it.
3) People are superstitious pattern matchers. We find patterns where they don’t exist. We like to analyze the world around us as if we are at the center of a purpose-driven universe full of nefarious and helpful agents. Whereas, most of the time, things happen not for “directed” reasons but they emerge from the behavior of collections of simple systems. We think what we had for breakfast affects the ups and downs of the stock market (and other such absurdities).
I’m sure the above list of reasons is not comprehensive and I could think of more with a little more thought (as could you or others). I don’t know exactly what people get from their varied religious beliefs, but I think it is highly resistant to intellectual challenge. New versions of spirituality that shun the trappings of organized religion are every bit as resistant to the challenges of evidence and reason. They are “personalized” (cherry-picked) religions that assemble the bits and pieces of other belief systems into some kind of whole that satisfies the individual. I’ve met no two “spiritual” people who share the identical core beliefs, though there are “constellations” of common belief subsets.
Hope that makes sense – Paul
Hi, I have one more question while I have your attention, I feel lucky to be able to ask questions directly to a well thought of author, although I just learned of you.
As an author you use allegory and imagery in your science fiction work, however this is in describing a fictional universe. Do you think using allegory and imagery rather than concrete language to describe our actual universe and day to day reality is in conflict to physicalism and empirical reasoning? For example songs or poems which describe normal phenomena such as relationships as something bigger.
Similarly a lot of spirituality could simply be seen as allegory of people describing their relationships with the world. I guess I am mainly wondering How can we differentiate the allegory of art and human expression from spirituality and religion?
Also your previous answer helps me feel confident that the best path to understand the world is to commit yourself to learning through empirical evidence rather than shortcuts through mysticism.
Hi Nader,
Certainly, there’s room for allegory and imagery (also analogy and metaphor) in helping people understand things better. However, we must be careful that people never take some interesting way of saying something as literal.
The physicist Werner Heisenberg is famously thought to have said: “The first gulp from the glass of natural sciences will turn you into an atheist, but at the bottom of the glass God is waiting for you.” That’s certainly laden with imagery and nice metaphors. Literalists could interpret it as saying “God is at the bottom of a glass”. Sounds stupid and even implausible that anyone would interpret that literally, but I’ll show another more subtle example soon where exactly that happens. Now we have no record how Heisenberg may have concluded that when science has produced so many examples that contradict the God of the Abrahamic religions (movement of planets, nature of stars, evolution of organisms, etc.).
I’ve argued that religion and science are perfectly tolerant of each other…until the next time science discovers something that disagrees with current religion dogma. Then there’s a period of readjustment of religious beliefs (keeping the gaps in our knowledge for “God” to fill in, of course) and things resume as they were.
Now for the more reasonable example. As a biologist, I’ve been guilty (as have many of my colleagues) of saying things like, “A bird’s wings aren’t designed to hover.” Of course, almost none of us really mean designed. Many of us simply use that has a short hand for something like: “have evolved under particular selective pressures” when we say “designed”. Professional biologists understand this and will mostly defend their real intent.
But, I’ve seen many Creationists, supporters of intelligent design, use this as proof (proof!) that most biologists believe in intelligent design. That’s the danger of using the wrong words; some literalist idiot out there will always be happy to abuse your casual language in ways no intelligent person could imagine.
Another example. People have said things like “Love is the energy that binds all humanity together.” Great phrase, expressing some important ideas. But, love is not an energy; it isn’t even a thing (it’s a concept, and a confused one at that); it doesn’t bind us but it is descriptive of certain long term relationships between people. Yet, others managed to extend this only slightly inaccurate phrase to something stupid: “Love is the energy that binds the universe together.” That literalist interpretation is so absurd as to be meaningless nonsense. This first phrase was an allegorical use; the second one is mystical garbage.
So, while I’m okay with waxing poetic in fiction, I work hard to be precise where needed. We need to especially be careful of extrapolating colorful sayings into domains where they don’t belong.
Hope that helps – Paul