Circadian Rhythms and the Clock Metaphor: Where the metaphor works & where it falls apart

We often describe the body’s timekeeping system as a “clock,” but how accurate is that metaphor, and what happens when we take it too literally?

In circadian biology, clock metaphors are everywhere. They offer a useful shorthand: rhythms, cycles, ticking along through time. But beneath the surface, the circadian system behavior diverges from the wristwatch on your arm or the clock on your wall. Even under stable conditions, it’s more dynamic, more complex, and more responsive than most clocks we know.

This piece unpacks where the metaphor works and where it misleads. To understand the biological clock, we have to look beyond the metaphor and into the dynamics of timekeeping in the body.

What is a clock?

To understand where the “biological clock” metaphor holds, and where it doesn’t, we first need to define what we mean by a clock.

At its core, a clock is any system that keeps regular time intervals. Early clocks were rooted in nature: people tracked the passage of time based on sunrise, sunset, and the movement of celestial bodies. Communities would ring bells at set intervals to mark time, each chime a phase marker for shared daily activities.

Eventually, clockmaking shifted toward precision. Mechanical watches introduced continuous timekeeping, and today’s digital clocks, synced by satellites and atomic time standards, offer extraordinary accuracy and consistency.

We’ve come to expect a few key features from clocks in the modern world:

• A constant period, typically 24 hours

• A uniform ticking rate, such as one tick per second

• Symmetry in response, clocks behave the same no matter when you adjust them

• The ability to be reset instantly to any time

These properties are ideal for organizing daily life: coordinating schedules, transport, communication, and shared time zones.

But biology plays by different rules.

A biological oscillator is a system that cycles through internal states autonomously. These systems:

• Are governed by feedback loops

• Are self-sustained (they continue even without external input)

• Respond to external cues

• Often behave non-linearly, meaning their output doesn’t scale in a simple way with input

They can also exist across multiple scales from within cells and organs to across the whole body, and on multiple timescales:

• Ultradian (faster than 24h)

• Circadian (about 24h)

• Infradian (slower than 24h)

A biological clock is a special type of oscillator that tracks time internally and continues cycling even in constant conditions. It can coordinate processes within and between systems, and it can also entrain to external cues like light.

The suprachiasmatic nucleus (SCN) in the brain is often referred to as the central circadian clock because it does all of these things: it sustains time internally, synchronizes to the outside world, and coordinates rhythms across the body.

Where the clock metaphor works

Despite its limitations, the clock metaphor holds up remarkably well in a few key ways, especially when describing the central circadian clock in the brain.

The SCN ticks with near-24-hour rhythms, generated through molecular feedback loops that cycle predictably and self-sufficiently. Even in constant darkness, these rhythms persist, one of the clearest signs of a true internal timekeeping system. Like a mechanical clock, the SCN:

• Keeps time consistently (endogenously, with a period close to, but not exactly, 24h)

• Coordinates other processes on a regular schedule (e.g., alertness, melatonin secretion, body temperature)

• Can be reset by environmental input, most notably light

In this way, the SCN functions much like a central clock, orchestrating temporal structure throughout the body. The clock metaphor helps convey this coordination, regularity, and resilience.

It also captures the predictive nature of the circadian system. Just like a clock tells us what hour is coming next, the SCN anticipates daily environmental cycles and prepares the body accordingly.

While the central clock provides a robust framework for understanding circadian timekeeping, the system is not as rigid or uniform as the metaphor suggests. The next layer of complexity, and where the metaphor starts to break, is how the circadian clock responds to its environment.

Where the metaphor breaks down

For all its strengths, the clock metaphor begins to falter when we look closely at how the central circadian clock responds to input, especially light.

Most mechanical or digital clocks have simple, predictable behavior. If they’re running fast or slow, you can reset them instantly, and they’ll resume without consequence. The timing of that reset doesn’t matter; behavior is symmetric and linear.

Not so with biological clocks.

Asymmetry in Light Response

The circadian system is phase-dependent, meaning its response to light depends on when the light is received. Light in the biological night causes phase delays (shifting rhythms later), while light in the early morning causes phase advances (shifting rhythms earlier). Midday light? It has little effect.

This pattern is captured by what's known as a Phase Response Curve (PRC), a concept without a counterpart in mechanical clocks. Crucially, the response is asymmetric and non-linear: it's typically easier to delay the clock than to advance it, and the magnitude of these shifts isn’t equal.

This helps explain why flying east feels harder than flying west, and why waking early is harder than staying up late.

Gradual Adjustment, Not Instant Resetting

Another key divergence: circadian clocks cannot be reset instantly. They adjust slowly over time, typically by no more than 1–2 hours per day. This gradual adjustment is due to the biological constraints of the feedback loops driving the rhythm. Attempts to shift too quickly (e.g., flying across time zones, rotating shift work) often result in misalignment, where the biological clock falls out of sync with the needs of the outer world.

No matter how well you “set” your alarm, your biology may not cooperate.

Why It Matters: Practical Implications

Understanding where the clock metaphor succeeds, and where it fails, is more than a philosophical exercise. It shapes how we think about health, performance, and the design of our environments.

1. Jet Lag and Shift Work Aren’t Just Inconveniences

Because biological clocks can’t be reset instantly, people working rotating shifts or flying across time zones experience genuine physiological misalignment. This isn't just fatigue. It’s disruption of hormone release, metabolism, and even immune function. Designing shift schedules and travel recovery plans requires understanding biological limits, not just adjusting external time.

2. Light Isn’t Neutral

Light at the wrong time can shift your circadian clock, altering sleep timing, alertness, and metabolism. If we think of light as just another environmental condition, we miss its role as a biological input. Timing matters as much as intensity.

3. Personalization Over Precision

Because circadian systems are plastic and phase-dependent, there’s no single “perfect schedule.” Chronotype, age, and recent light exposure all influence the rhythms your body tries to keep. That means strategies for optimizing performance, sleep, or metabolic health should consider individual rhythms, not just diurnal time.

Beyond the Metaphor

The clock metaphor got us far by giving us language to describe internal rhythms and making the science relatable. But to move forward, especially in an age of wearables, light-based interventions, and 24/7 culture, we need models that reflect how circadian systems actually behave. They adapt, shift, anticipate, and sometimes fall apart.

The more precisely we understand biological time, the better we can design systems that support it. If we want to live in better sync with our biology, we need to stop thinking like watchmakers and start thinking like systems engineers.