Do we have a soul?


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.

* * *

Indian Arm from Burnaby Mountain

Indian Arm from Burnaby Mountain

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.”

Do we have an eternal soul?

Do we have an eternal soul?

“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.”


“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.”

Sub-atomic particles can be forced apart by energetic collisions

Sub-atomic particles can be forced apart by energetic collisions

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.”

Human and chimp DNA is 98% identical

Human and chimp DNA is 98% identical

“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.”

This "brainbow" image shows neural interconnections

This “brainbow” image shows neural interconnections

“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.

Knowledge representation: a Simpsons conceptual network

Knowledge representation: a Simpsons conceptual network

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.

More on this later.


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About Paul Anlee

When I was very young, a teacher asked our class to write about what we wanted to be when we grew up. My story was titled "Me the Everything." I've been fortunate to come close to fulfilling that dream in my life. Computer programming, molecular biology, nanotechnology, systems biology, synthetic biology, mutual fund sales, and photocopy repair; I've done them all. I've spent way too much of my life in school, eventually earning degrees in computing science (BSc) and in molecular biology and genetics (PhD).After decades of reading almost nothing but high-tech science fiction, I decided to take a shot at writing some. I aim for stories that are true to the best available science, while pushing my imagination far beyond the edge of what we know today. I love biology, particle physics, cosmology, artificial intelligence, cognitive psychology, politics, and economics. My philosophy is empirical physicalism and I blog regularly about the science and the ideas found in my novels. I believe fiction should educate and stimulate, as much as it entertains.I currently live in Cuenca, Ecuador where I study Spanish and Chen-style Tai Chi , when I'm not working on exciting and provocative new stories. Visit my web site and blogs at
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One Response to Do we have a soul?

  1. bhupendra says:

    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?

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