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Scientists Discover Why Toxic Thoughts Run Rampant When We're Tired
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Scientists Discover Why Toxic Thoughts Run Rampant When We're Tired

A study shows what happens in our brain to allow negative thoughts to flourish when we're sleep deprived.

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Katrina Paulson
Apr 22, 2025
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Scientists Discover Why Toxic Thoughts Run Rampant When We're Tired
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Hiya!

Have you ever done something embarrassing? Like, really embarrassing? Something so uncomfortable that the memory haunts you long after the event? I sure have. And somehow it’s even worse when I’m sleep-deprived, making it harder to keep the memory at arm’s length.

This link between poor sleep and intrusive thoughts has been elusive, but recent research brings us closer to an answer. And, it turns out that a lack of sleep does indeed make our brains less efficient at keeping unwanted thoughts out of our conscious mind, and likely also contributes to the onset and continuation of mental health struggles.

Memory Containment and Retrieval

Side note: I’m including a bit more than is necessary in this section simply because I think it’s interesting, but feel free to skip ahead.

We don’t have just one type of memory, and there isn’t only one area in our brain that stores them. We experience several kinds of memories, and they’re stored in interconnected regions across our brain.

First, we have our long- and short-term memories. Short-term memories last less than a minute before basically being deemed unworthy of long-term storage by our brains. Meanwhile, our long-term memories are further filtered into conscious (explicit) or unconscious (implicit) memories.

Our implicit memories include procedural ones, involving motor (movement) skills, such as playing sports or typing on a keyboard. Priming memories are also implicit and are formed when we connect one stimulus to another, like how the words “toothbrush” and “tooth paste” are associated with each other more than, say, “toothbrush” and “recliner.”

Our explicit, or conscious memories, include episodic memories, which are our experiences or the ‘episodes’ of our lives, and our semantic memories, such as facts and general information we learn about the world.

It’s all a bit overwhelming, but I found this handy-dandy illustration by Australia’s Queensland Brain Institute that helps make sense of it all.

Image Source: Queensland Brain Institute

Further, different types of memories are stored in different brain areas. Our implicit, or unconscious, memories are primarily stored in the basal ganglia and cerebellum, which makes sense since both regions involve our bodily movements (as well as other functions such as emotional regulation and learning).

Meanwhile, short-term memories mostly rely on the prefrontal cortex, which is involved in all sorts of essential things, including being the control center for our “executive functions,” such as thinking and problem-solving, while also supervising and directing other areas of the brain.

However, it’s our explicit or conscious memories that we’ll be focusing on today, which include our experiences (episodic) and the general information and facts about the world that we know (semantic).

Such memories are stored in not one, not two, but three brain regions: the neocortex, the amygdala, and the hippocampus. All three of which are highly involved in our emotions, learning, and, of course, memory.

The neocortex is the newest part of our brain and takes up 90 percent of our cerebral cortex. It’s responsible for higher-order brain functions such as thinking, movement commands, spatial reasoning, language, and sensory perception. It also plays an essential role in processes like memory, learning, and decision-making.

The amygdala is a small, almond-shaped region that helps regulate our emotions, especially fear, and connects our emotions to our memories, learning, and senses. It tells us what’s dangerous and instigates our fight-flight-or-freeze response.

However, the hippocampus is especially significant because, more than the other brain regions discussed so far, the hippocampus is perhaps the most involved with our memories. Each brain hemisphere has a small sea-horse-shaped hippocampus, and together, they are essential to creating our memories and are responsible for transferring them from our short-term to long-term storage.

The hippocampus is also highly involved in retrieving our memories, along with another part of the brain called the right dorsolateral prefrontal cortex (rDLPFC). (Remember the rDLPFC because it’s a big part of the research I’ll tell you about soon.)

One way to think about it is to imagine the hippocampus as a storage room for your memories. But your memories don’t sit calmly on the shelves waiting patiently for retrieval. No, they bounce around like toddlers on a sugar high. So, the storage unit needs a door to keep them all inside, which is the role the rDLPFC plays.

Memories and Sleep

Okay, now that we better understand the types of memories we form and where they’re located in our brain, the next thing is to understand the mechanics of it all.

Sleep is perhaps the most essential factor for a successful, smooth-running memory consolidation process. Yet, it’s also one of the more mysterious systems.

Researchers believe sleep provides the ideal conditions for the brain to consolidate our memories because it’s not being bombarded by external stimulation. Without such distractions, the brain can increase neurotransmitter activity to facilitate higher levels of communication between the neocortex and hippocampus.

Sleeping may also give the brain a break, allowing it to weed through memories that are no longer useful to make space for new, more relevant memories. Research suggests that various types of memories are processed in multiple brain regions during different stages of sleep, particularly during deep sleep and while dreaming.

Studies also show that our brain replays our experiences, like playing a video of our days, as we sleep. This process helps the brain sort through and consolidate our memories, strengthening them while supporting our creativity, emotional regulation, and problem-solving abilities.

How does the brain achieve all of this, precisely? According to George Dragoi — an associate professor of psychiatry and neuroscience at Yale School of Medicine, who studies how episodic memories form and develop — there appear to be two parts, or phases of the process: encoding and then consolidating our memories.

Part One, Encoding Memories

Research by Dragoi from 2018 shows that during our daily experiences, cells in our hippocampus fire in “unique and novel” rapid sequences that flush out the details of our memories and encode the experiences within the hippocampus neural networks.

Meanwhile, the amygdala appears to attach emotional significance to the details of our experiences. And speaking of emotions, they are the crux of our memories as we typically only remember the experiences that emotionally impact us the most — the good and the bad — because they help us survive. Otherwise, we’d struggle to remember what’s safe or dangerous.

Part Two: Memory Consolidation

After encoding the details and emotional aspects of our experiences into memories, the next phase is to consolidate them. Researchers believe this also happens when we sleep, particularly during slow-wave sleep, the deepest sleep stage.

Slow-wave sleep accounts for between 10 and 20 percent of the time adults spend sleeping, with each cycle lasting around 20 to 40 minutes.

During this period, it’s believed that the brain takes the previously encoded memory sequences, integrates them using chemical connections into new and existing neuronal knowledge networks, and then files them into long-term storage.

Intrusive Thoughts

So, what does any of this have to do with why intrusive thoughts bombard us? As Scott Cairney, an associate professor of psychology at the University of York in England, and a senior author of the study I’ll tell you about soon (I promise), explains that when the two memory formation phases work well,

“Memories of unpleasant experiences [will] often intrude into our conscious mind in response to reminders, but tend to be fleeting and can be put out of the mind again.” Meanwhile, “[s]uppression is a very clever function of the brain as it weakens all of the connecting traces of the memory, thereby inhibiting us from joining up all the dots to retrieve the full picture of the experience when it is triggered by an external stimulus.”

Unfortunately, this process doesn’t always work as well as we’d like. Sometimes we forget things we’d like to remember, and remember what we’d rather forget.

Marcus Harrington, a Lecturer in Psychology at the University of East Anglia in England, who specializes in research into sleep, memory, and emotions, and is the new study’s other senior author, said,

“While such intrusive memories are an occasional and momentary disturbance for most people, they can be recurrent, vivid, and upsetting for individuals suffering from mental health disorders such as depression, anxiety, and post-traumatic stress disorder [PTSD].”

Cairney and Harrington have long been curious about this issue and have spent years researching it.

Previous Research

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