Paley’s Watch Found

There actually is a clock in the heath, and it’s in our bodies, too.

What is a watch? It’s an instance of a clock. William Paley famously presented his famous “watchmaker argument” in Natural Theology in 1802, a book that influenced Darwin. Paley asked what one could deduce if he ran across a watch lying upon the ground in a heath. With cogent analysis, he anticipated the arguments of Michael Behe (Darwin’s Black Box) about irreducible complexity and arguments about functional wholes of Douglas Axe (Undeniable). Whether or not Paley took his argument too far, his “watchmaker argument” can stand on its own as a logical argument for intelligent design.

Since a watch is a clock, but not all clocks are watches, we need to be sure that other instances of clocks support Paley’s argument. One might dispute Paley by saying the daily rotation of the earth is a ‘clock’ of sorts that is not irreducibly complex. The point of the argument is that a designed clock has a point. It’s organized in a way to tell time for a purpose. The earth’s diurnal cycle is oblivious to beings that might use it to tell time, but a watch was made for the purpose of monitoring the passage of time for human use. The Greeks had a water clock. Early medieval people had the hourglass. Christian Huygens invented the pendulum clock. As science progressed, clocks utilizing springs and gears, then quartz vibrations, and then atomic frequencies refined timekeeping to astonishing levels of accuracy. Timekeeping devices are so accurate now that scientists routinely have to consider adding a “leap second” every few years to keep instruments in sync with astronomical phenomena, and GPS satellites have to take very tiny relativistic effects into account.

Critics of Paley might say that the early timekeeping devices, like the hourglass, are not irreducibly complex (IC), because any similar repetitive process in nature could be used by a person to infer time, even if it doesn’t happen for the purpose of providing timekeeping information to humans. Examples might be tides, the rising and falling of the Nile, or a regular geyser’s eruption. At some point, human clock devices certainly became IC, because nobody would assume nature could produce a modern atomic clock.

One telltale sign of an IC clock mechanism would be if it contained switches that perform a function. Most of us have seen the mechanical trippers on certain clocks that flip lights on and off. Alarm clocks that turn on a buzzer or radio station are more examples. These days, the clocks in our smartphones can switch on all kinds of applications, and the “internet of things” is beginning to link whatever function one might desire to the passage of time, so that you can even reset your home lights in New York remotely from a Paris cafe. Hourglasses lacked these additional functions. Whenever we see a clock that can switch on another function that is independently useful, we’re getting close to IC. If it can switch on numerous functions, and simultaneously respond to external inputs to keep those functions regulated within tight constraints, then the case for IC becomes very convincing. If Paley’s 1805-era watch was IC, how much more would such a time-based, adapting, switching master regulator be?

The Circadian Clock

Now we are ready to announce the existence of such a clock: the circadian clock in all living things. Science Magazine published a collection of papers on biological clocks recently. In a leading Perspective article, Millius and Ueda discussed why organisms need circadian mechanisms, and how new knowledge is being gained about them:

An internal biological rhythm, the circadian clock—which can be measured by changes in rhythmic gene expression, cellular activity, or physiological behavior—enables an organism to anticipate daily cyclic changes in the environment.

Credit: Illustra Media

We see in this quote that the clock mechanism comes from genes, which are sequences of information – not mere rhythms of natural objects subject to laws of nature (like the tides). We see also that these genes switch on functions such as cellular activity or behavior that are important for the organism. The genes can adjust to external inputs, such as sunlight, as when we adjust to jet lag. The functions that the circadian clock switch on are numerous, the article goes on to say. Effects occur at all scales, too, from the individual protein and organ to the whole organism. Even more interesting is the finding that timekeeping functions differ between tissues. This suggests that the regulation of circadian rhythms are customized for each tissue, for each organ, and for the whole organism (e.g., for diurnal and nocturnal animals). Here’s a sample of the complexity researchers found when they measured gene expression in the tissues of one species of primate, the olive wild baboon:

Approximately 11,000 transcripts were expressed in all 64 sampled tissues, which the researchers called ubiquitously expressed genes, including many involved in basic cellular functions such as DNA repair, transcription, and protein homeostasis. Most of these ubiquitously expressed genes were rhythmic in at least one tissue, but there was little overlap in rhythmic genes between tissues, which suggests that tissue-specific mechanisms control oscillatory expression. For example, a gene that had rhythmic expression in the liver was constitutively expressed in the heart. Because ubiquitously expressed genes control fundamental biological processes, timing their expression can affect the overall function of a tissue. For example, diurnal regulation of exocytosis in the thyroid or adrenal glands may enable rhythmic release of endocrine factors, compared with other organs in which the timing of exocytosis is less important for function.

The Whole-Genome Clock

Credit: Illustra Media

In another Perspective article by Carolina Diettrich Mallet de Lima and Anita Göndör in Science, we learn that the whole genome itself is organized to facilitate circadian homeostasis, that is, the maintenance of accurate timekeeping in spite of external perturbations.

Maps of physical contact probabilities between distant regions have earlier revealed that the genome is organized into topologically associating domains (TADs) displaying high local, intradomain chromatin-fiber contact frequencies. Given that TADs constrain and thereby increase the specificity of enhancer-promoter (E-P) contacts, the mechanisms and dynamics of TAD formation are intensely investigated.

This organization that regulates gene expression is highly specific, as would be expected for homeostasis. But it also exhibits flexibility. The Perspective article references a paper in Science by Kim et al. that shows that the circadian clock is not only reliable, it is able to adapt to changing conditions.

Phenotypic plasticity, the potential for phenotypic change in response to external signals, drives adaptation to environmental fluctuations and requires flexible gene regulation. A seminal example of adaptive plasticity is represented by the circadian clock, which establishes 24-hour rhythmicity in physiology, metabolic activities, and behavior. As external time cues, such as light and food intake, can reset the phase of oscillations, circadian homeostasis enables light-sensitive organisms to both anticipate and adapt to daily environmental cycles. On page 1274 of this issue, Kim et al. provide a glimpse into the genome-wide complexity of transcriptional plasticity during the physiological circadian cycle in mice, with implications for our understanding of diseases linked with deregulation of the circadian clock.

The Cell Cycle Clock

Another type of clock does not need to know the time of day so much as it needs to ensure processes occur in the proper sequence. Business project managers are familiar with Gantt charts or Pert charts that lay out the sequence of steps in a project, such as what steps need to complete before other steps can begin. A foreman on the project might establish checkpoints for go or no-go decisions based on upstream events. That’s what the cell does when its project is duplicating itself. Phys.org tells how proteins regulate the cell cycle:

Credit: Illustra Media

Cell division is the basis of all life. Even the smallest errors in this complex process can lead to grave diseases like cancer. Certain proteins have to be switched on or off at specific times for proper cell division. Biophysicists and medical biochemists at Martin Luther University Halle-Wittenberg (MLU) have described the underlying mechanism of this process. They report how different signaling pathways in the cell change the structures of proteins, thereby driving the cell division cycle in the right direction at the right time. The researchers present their findings in Proceedings of the National Academy of Sciences.

Lest anyone doubt that the cell cycle is irreducibly complex, read on:

The cell cycle is an extremely complex and precisely defined process. “The parent cell has to double its existing components and then divide into daughter cells. In order to do this, numerous genes have to be switched on and off at very specific times,” says biophysicist Professor Jochen Balbach from MLU. The cell cycle is sub-divided into phases. These are controlled by what are known as inhibitor proteins, also called CDK inhibitors. Like a red traffic light, these proteins block transition to the next phase until the cell gives the relevant start signal.

Conclusion

Paley’s watch has been found. It was inside him all the time, as well as inside the heather on the heath. The exciting thing is, it is far more complex than Paley could have imagined. If a relatively simple watch on the ground was sufficient to infer intelligent design, how much more the regulated, flexible, switching circadian clocks described above?

Exercise: Darwinians will undoubtedly rush to argue that there is an evolutionary path to the human circadian clock with all its complexity. Some early microbe found it beneficial to regulate its activity by the diurnal cycle. Later organisms got better at it, and over millions of years, here we are. How would you respond to this claim? (comments are invited). We have more to say about natural selection in a future post, but start with our March 13 entry, ‘Natural Selection? No – Sheer Dumb Luck.” The evolutionary comeback hinges on what ‘fitness’ means, and whether natural selection is a creative process with functional innovation as an expected outcome. It’s not enough to imagine a path and tell just-so stories about it. The actual random mutations that were selected need to be specified.

Extra Credit: Many skeptics feel that David Hume answered Paley’s argument from design and basically overturned the case of the natural theologians. Hume, however, wrote his Dialogues Concerning Natural Religion in 1779, a full 23 years before Paley’s book came out. Imagine a debate between Hume and Paley. Who do you think would have succeeded in 1802? Who do you think would win in 2018, now that we know much more about life, genetics and the living cell?