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“Astonishing” Clocks Found in Bacteria

Photo credit: Adam Bignell via Unsplash.

Science news from England speaks of the “Astonishing complexity of bacterial circadian clocks.” The astonished scientists hale from the John Innes Centre in Norwich, an “independent, international centre of excellence in plant science, genetics and microbiology.” Why would researchers in the UK and in mainland Europe, predominantly Darwinians, react with astonishment? It was from pondering how evolution could give accurate timepieces to the simplest, most primitive forms of life. 

Antony van Leeuwenhoek, the first to view bacteria with a simple microscope in 1683, was astonished to see life forms this small that were capable of motion and reproduction. William Paley in 1805 would have been astonished to be told that a watch on the heath simply emerged out of the ground. But today’s evolutionists take complexity for granted. Every tissue, organ, and system in biology can be accounted for by the omnipotent hand of natural selection. “Ho-hum” should be the reaction.

Bacteria make up more than 10% of all living things but until recently we had little realization that, as in humans, soil bacteria have internal clocks that synchronize their activities with the 24-hour cycles of day and night on Earth.

New research shows just how complex and sophisticated these bacterial circadian clocks are, clearing the way for an exciting new phase of study….

An international collaboration from Ludwig Maximillian University Munich (LMU Munich), The John Innes Centre, The Technical University of Denmark, and Leiden University, made the discovery by probing gene expression as evidence of clock activity in the widespread soil bacterium Bacillus subtilis. [Emphasis added.]

“Pervasive” Clock Activity

The authors published a paper about this in Science Advances, announcing that the bacterial clock “evokes properties of complex, multicellular circadian systems.” The lead author, Francesca Sartor, noted that the clock activity is “pervasive” in this tiny microbe. It regulates multiple genes and behaviors.

Professor Antony Dodd from the John Innes Centre added, “It is astonishing that a unicellular organism with such a small genome has a circadian clock with some properties that evoke clocks in more complex organisms.

Moreover, the researchers believe that clocks are widespread in bacteria. What happened to the notion of simple to complex evolution by gradual steps? Would a “blind watchmaker” start with a Rolex?

Professor Ákos T. Kovács, from Leiden University and Technical University of Denmark said… “it is amazing that the circadian clock in Bacillus subtilis — a bacterium with just four thousand genes — has a complex circadian system that is reminiscent of circadian clocks in complex organisms such as flies, mammals, and plants”.

“Just four thousand genes” sounds flippant. Try counting to four thousand out loud; it will take over two hours at two seconds per integer. As you count, think of a molecular machine, regulatory element, or purposeful role represented by every one of those digits. Each bacterial gene, moreover, is composed of 900 base pairs on average. That’s a lot of functional information packed into an organism a micron in diameter. Even so, evolutionary biologists did not expect to find circadian clocks in bacteria that match the functional sophistication of those in flies, mammals, and plants.

Are Genes Blind Watchmakers?

Audrey Mat, a marine biologist at the University of Vienna, says that genes are “The Great Clockmakers.” Writing in The Conversation, she gives the ho-hum response to the existence of timekeepers in living organisms. “The rotations of the Earth, Moon and Sun generate environmental cycles that have favoured the selection of biological clocks.” Under this reasoning, pressure waves favor the selection of ears. Photons favor the selection of eyes. Planet rotations and orbits favor the selection of clocks. Environments can favor things all they can, but complex sensors to detect and use them do not logically follow.

The circadian clock mechanism was first discovered in the fruit fly, also known as Drosophila, in the 1970s. It is based on feedback loops in the transcription and translation of several genes — gene A promotes the expression of gene B, which in turn inhibits the expression of gene A — creating an oscillation. During the day, light induces the diminution of specific factors of the loop via a photoreceptor called cryptochrome. Interestingly, the key factors in the mechanism essentially only comprise a few genes named period, timelessclock and cycle. However, the fine-tuning and regulation of the clock is based on a complex molecular and neuronal network that ensures its timing and precision.

According to Mat, physical forces not only drive the emergence of devices to sense them; they also tune them and maintain them. They even adjust their responses to the changing seasons. How does Darwinism explain this? It doesn’t:

The circadian clock is not the only clock mechanism that exists in nature. Many biological processes are seasonal, such as the migration of a host of birds and insects, the reproduction and hibernation of many animal species and the flowering of plants. This seasonality is generally dictated by several factors, including by what is known as a circannual clock in the case of many species. The mechanism of this clock has not yet been determined.

Can Clocks Be Darwinized?

The paper in Science Advances makes no claim for Darwinism, either. The authors put evolutionary explanations in future tense: 

Discovering mechanisms by which this memory of entrainment conditions during development of a circadian system occurs, in diverse systems, will inform on convergent and divergent evolutionary processes.

That’s all they say about evolution. Don’t hold your breath, though, for answers. Faced with complex functional timekeeping in the most primitive organisms, evolutionary biologists have their storytelling work cut out for them.

Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in nonphotosynthetic bacteria. Here, we describe an inherent complexity in the Bacillus subtilis circadian clock…. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing them as a general property of this species, and that its circadian system responds to the environment in a complex fashion that is consistent with multicellular eukaryotic circadian systems.

The complex abilities of the bacterial species included entrainment, or the following of cues. Like catching a train, entrainment requires sensing environmental cues, called zeitgebers, and getting on board to go somewhere on purpose. This also presupposes a memory of the cues. 

Starting Expectations and Startling Conclusions

One doesn’t always see “surprised” in a stodgy scientific paper, but the word stood out in this one:

Entrainment leads to the establishment of a stable phase relationship between the external (environmental) and the internal (circadian) time. Circadian systems use zeitgebers for entrainment, leading to a set of remarkable phenomena. We were surprised to observe that a prokaryote challenged with chronobiological protocols exhibits a variety of highly complex entrainment properties…. The presence of aftereffects (see table S1) suggests that information regarding zeitgeber exposure is stored, much like a memory.

They didn’t expect this. “It would be naïve to assume that a prokaryotic circadian clock shares these properties with multicellular organisms,” they initially thought, but the observations proved otherwise. Using red and blue light as zeitgebers, and watching responses with fluorescent cues, they were able to entrain the microbes and alter their behaviors by modifying the free-running period (FRP) of the light. The results demonstrated that “this organism shares many circadian characteristics occurring in eukaryotic organisms, some of which have yet to be documented in established clock models in cyanobacteria or fungi.” 

Our observations also underscore that a combination of zeitgebers is used by B. subtilis, which is analogous to the situation for fungal, mammalian, and plant cells. The task of the circadian clock is to “read” the local environment and, for many systems, this means harvesting not just one but many cues. We suggest that by using both blue and red light and temperature as zeitgebers, B. subtilis can fine-tune clock-regulated processes to a greater range of situations.

For this to be true of tiny microbes that live in the soil is indeed surprising. How do they do it without eyes? The “light-sensing mechanisms used by B. subtilis for the purpose of entrainment remain unknown.” Perhaps the microbes respond to the energy levels of different wavelengths of light penetrating the soil. Whatever is involved in the bacterium’s clock led to a second use of the word “remarkable” in the conclusion:

In conclusion, we find it remarkable that a relatively simple prokaryote, which lacks the obvious hierarchy of organization of multicellular organisms, evokes properties of complex circadian systems.

Design advocates would certainly find it remarkable, too. But surprising? For those committed to explaining biology by unguided material causes, surprise is understandable. Those who recognize the hand behind the superb engineering all around us in life are delighted but not surprised.