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Journal of Creation 34(2):105–110, August 2020

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Circadian rhythms and creation

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A large number of organisms possess operational systems that vary in intensity in a rhythmic manner over a 24-hour period. These circadian rhythms usually are entrained by light and are vital for the robust functioning of the organism. The immediate interest for us is the origin of the regulatory system underlying circadian rhythms. The regulatory systems responsible for rhythmic phenomena can be complex, especially in plants and animals. No transitional schemes can be constructed to explain the emergence of the more complex systems from the simpler ones found in bacteria on account of lack of homologous features conserved across the kingdoms. In laboratory experiments, considerable design input is needed to construct the simplest artificial biological clock; these do not run on a 24-hour cycle. The existence of circadian clocks, with fundamental common design elements, specified complexity, and functional coherence, argues for the existence of a designer.


clocks

Many biological processes show regular self-sustained cycles of approximately 24 hours. These are termed circadian; the cycles are regulated by cellular clocks. The features that usually are taken to characterize circadian clocks are that they operate on a self-sustaining basis and show approximately 24-hour oscillations under continuous conditions of either constant light or darkness. Genuine rhythms show temperature compensation—stability of the rhythm over a range of temperatures. Circadian rhythms have been observed from photosynthetic bacteria, fungi, insects, and plants, to mammals operating under natural conditions.1,2

Diurnal rhythms in plants have been known from ancient times (400 BCE). These rhythms, now recognized as circadian, synchronize various physiological functions to the 24-hour rotational cycle of the earth. Much later, unicellular bacteria and eukaryotes, including humans, were shown to possess circadian clocks.3 We understand that temporary disturbances are adjusted readily, as indicated by recovery from jet lag in humans.4,5

Significance of clocks

The clocks have significance to all forms of life possessing them. In mammals the daily clocks regulate a range of functions and behaviours, from cell division to blood pressure, hormone release, digestion, immune function, and cognition. In these organisms there is a master clock and each of the cells has an independent clock.3,6

Disturbance of the circadian clock can lead to some serious outcomes. Experimental animals subjected to disruption of the circadian clock through mutation or deletion of the appropriate genes show altered physiology and behaviour. Pathologies may develop, such as metabolic dysfunction, cancer, premature ageing, cardiovascular, and renal abnormalities. 7

In one large study in humans (433,268 adults), lifestyle differences were analyzed. The contrast was between those individuals where activities (work and social) were organized for the evening (late timing of sleep and generally shorter sleep durations), with those possessing a morning emphasis and early sleep appointments. An increased risk of mortality was shown in the evening types with an elevated risk of cardiovascular events, diabetes, and psychological, neurological, respiratory, and gastrointestinal disorders.8 Disruption of circadian rhythms through lifestyle choices and light pollution can change the rhythmic levels of circulating melatonin and cortisol in the body and also interrupts the rhythms in bone growth leading to weakened bones.9,10 Credible evidence is accumulating to suggest that both the rate of ageing and the progression of some age-related diseases are related to the disruption of circadian rhythms and melatonin levels.10

Certain mental illnesses are associated with the disruption of the circadian cycle. The strategy of resetting it by forced regulation of sleep may result in a reduction of psychotic episodes in about half of schizophrenia patients. Not only is disease progression faster when schedules are not synchronized to the internal clock, but also the effectiveness of certain drugs may be time-of-administration dependent.11

The minimal clock in cyanobacteria

Cyanobacteria possess a relatively simple circadian clock consisting of three essential components (this contrasts with a component rich scene with the so-called higher organisms). Similar photosynthetic prokaryotes are considered to have played a critical role in evolution of the plastid. Evolutionists presume that ingestion of a cyanobacterium took place by a mitochondrion-containing eukaryote, leading to the evolution of plastids as a consequence of the endosymbiotic relationship thus established.12

Now cyanobacteria contribute to the maintenance of an oxygenic environment, but the clocks allowed adaptation to fluctuations in the environment. These organisms possess a minimal time-keeping system regulated by a small cluster of genes. The circuitry responsible for the oscillations is a post-translational circuit type.13

The clock system involves an oscillator that is connected with the timing loop. An input pathway is present for sensing environmental signals and transmitting them to the oscillator, and an output pathway also exists that transmits information from the oscillator to influence cellular activities.14

Oscillator and timing loop. The timing clock in the cyanobacterium Synechococcus elongatus and a few other cyanobacteria consists of three proteins (KaiA, KaiB and KaiC) encoded by the KaiABC gene cluster. A genuine circadian clock operates in such organisms, as the oscillator can be reconstituted in vitro when the three purified proteins are in the presence of ATP. The stable oscillations shown are of 24-hour duration. Moreover, the pacemaker operates on a 24-hour cycle despite the fact that the generation time of the organism can be as short as 5–6 hours. Remarkably, the clock of the daughter cell operates in phase with that of the mother cell.15

Image: 2018 Nicolas M. Schmelling and Ilka M. Axmann, Royal Society/CC BY 4.0fig-1
Figure 1. Circadian clock operation in Synechococcus elongatus. Protein KaiC is the central oscillator. Its phosphorylation state determines its interaction with other key proteins (KaiA and KaiB). KaiC autophosphorylation is stimulated by KaiA. Fully phosphorylated KaiC interacts with KaiB, which then initiates loss of phosphate. KaiC drives the transcription of the kaiBC operon through the phosphorylation of the histidine kinase SaSA and the DNA binding protein RpaA. A negative feedback loop in the process is driven by a bacteriophytochrome protein, CikA, and involves repression of RpaA activity.19

A key gene regulates KaiC protein production that goes through oscillations in phosphorylation to initiate circadian rhythms. KaiC undergoes autophosphorylation during the day in the presence of adenosine triphosphate when stimulated by KaiA (figure 1). At night autodephosphorylation occurs when KaiA is inhibited by KaiB. This process takes hours to complete. The cyclic nature of the phosphorylation states is vital. However, the processes involved in the operation of this cycle are far from simple. In fact, there are detailed conformational changes involved in the interactions that occur among the Kai proteins. It has been shown that the key protein in the cycle, KaiC, the central pacemaker, undergoes a slow tightening and loosening of a particular ring structure following autophosphorylation. This gives KaiA and KaiB proteins access to specific binding domains on KaiC. It is noted that the tight binding aspect is vital to the success of the process. Nevertheless, there is competition for binding sites among other components of the system and KaiB must also undergo conformational changes to allow the formation of the KaiB-KaiC complex. Overall, the changes, which are quite detailed, allow the clock to measure time between sunrise and sunset.11,16,17

The circadian oscillation of KaiC phosphorylation can be enabled in vitro as indicated previously. This shows that a transcription/translation feedback loop is not essential to the circadian oscillation mechanism. The oscillator functions independently of transcription. However, a regulatory feedback loop is essential for normal growth in the natural environment as it links the post-translational oscillator to the transcription machinery (figure 1).18

Input pathway. Environmental cycles entrain the circadian clock. This means that a dark pulse intervention in an otherwise environment of continuous light will reset the clock. One key protein associated with the input pathway is circadian input kinase (CikA) that monitors the redox status of cells and light intensity.14

Primary output pathway. The expression of the circadian genes (kaiBC) centres on the histidine kinase SasA and a response regulator protein, RpaA, which can bind to DNA. The histidine kinase autophosphorylates following KaiC binding. The phosphate is then transferred to the master regulator RpaA, which is the transcriptional activator. The operation of this system is necessary for normal growth of the cyanobacterium. Secondary output pathways have also been identified.18,20

Complex clock in plants

Plants live in an environment that changes on a regular basis as day follows night. The environmental changes associated with the rotation of the earth are linked with many rhythmic phenomena in plants.

As in the cyanobacteria, circadian clocks in plants involve an input pathway (photoreceptors), a circadian clock mechanism, and output pathways giving rise to rhythmic behaviour (figure 2).

fig-2
Figure 2. Conceptual scheme showing the flow of information in circadian clocks.21

In contrast to the relative simplicity found in the cyanobacteria, the situation in land plants is complex. Multiple photoreceptors (phytochromes and cryptochromes) have been identified and there are also sensors for other stimuli. Instead of one central post-translational oscillator, as in cyanobacteria, oscillation in gene expression is achieved through transcription-translation feedback loops.

The circadian clock consists of interconnected feedback loops (positive and negative—figure 3). The interlocking system found in the model plant used in research, Arabidopsis, is very complex, surpassing the complexity found in fungi and animals. More than 20 interlocking transcriptional feedback loops are involved in contrast to the relatively few found elsewhere in eukaryotes. This is postulated to have evolved to give such sessile organisms the ability to contend with environmental extremes.21,22

How did the clocks arise?

Circadian clocks often are very complex as noted in the last section. Explaining the necessity for such clocks has been challenging. Although a raft of supposed evolutionary benefits can be listed for organisms possessing these clocks, the list can be shortened. The primary basis for circadian clocks presumably resides in the resistance to environmental fluctuations it gives to organisms.3

The construction of even a rudimentary oscillator can be challenging. Elowitz and Leibler were able to construct a rudimentary oscillatory network using components found naturally in other situations.23 This they accomplished by constructing a plasmid with three repressor components, which gave a periodicity in the delivery of a product (green fluorescent protein) of around 150 minutes when inserted into Escherichia coli. Although the plasmid was transmitted from generation to generation, the variation in periodicity between cells could be considerable. This surely indicates the difficulty of constructing a viable scheme for the emergence of oscillatory systems through chance events.

fig-3
Figure 3. Positive and negative interlocking feedback loops characteristic of circadian clocks in most organisms.21

In Elowitz and Leibler’s feedback loop, each gene produced a protein that repressed the next gene in the loop. The repressor network constructed involved first LacI from Escherichia coli. This repressor protein inhibited the transcription of the second repressor gene tetR. Its protein product inhibited the expression of the third gene, cl. And, finally, CL protein inhibited lacI gene expression. There was an irreducible complexity to the working of the clock. Since this work involved synthesizing a regulatory network, it follows that there was a predictable, minimal design aspect involved. Indeed, the authors held that improving the design of such artificial systems might allow an understanding of the ‘design principles’ needed for the clock to work in evolved organisms occurring naturally. Interestingly, a set of three inhibitory interactions of a regulatory nature are noted as being critical to keep the network rhythmic in mammals. In this respect, the design is like that used by Elowitz and Leibler in their synthetic repressilator. A similar motif has been suggested as functioning in plants.23,24

Bearing in mind that eukaryotes show circadian rhythms, it is reasonable to anticipate some similarity in genome structure driving this function among the simpler organisms from which they allegedly arose. None of the Kai proteins identified in prokaryotes shows sequence similarity with proteins found in eukaryote clocks. Also, extensive analysis has shown that components in archaea, bacteria, and cyanobacteria (prokaryotes) responsible for rhythmic genes differ substantially, with KaiA protein often lacking and with differences in input and output mechanisms being noted.25,26

Homologs of kaiB and kaiC genes have been found in a number of prokaryote genomes, but their function is not understood beyond suggesting that having these genes confers some type of enhanced adaptive fitness. However, no eukaryotic organism carries Kai proteins, making the creation of meaningful links with this putative group of prokaryote ancestors difficult.14,25,27 Significantly, the circadian clock in the cyanobacterium S. elongatus functions as a post-translational oscillator where the association of KaiA and KaiB drive phosphorylation of KaiC, which is an auto kinase, phosphorylase, and ATPase. A feedback loop has been identified regulating the phosphorylation state of key proteins. This is essential for normal growth in the natural environment as it links the post-translational oscillator to the transcription machinery. This process differs somewhat from that seen in plants and animals. There, clock operation is via interlocking transcription-translation feedback loops. However, some post-translational control of circadian activity is involved in plants, fungi, and animals.1,28,29 This means that many organisms possess circadian clocks that use both transcription-translation and post-translational steps to enable functioning in the natural environment.30

The emergence of circadian clocks, as seen in eukaryote cells, demands the presence of compartmentalization. The existence of membranes hence is vital in that this allows separation of reactants and products and also provides for events to happen at different times.11 Explaining the emergence of complex clocks found in plants and mammals requires the sorts of developmental gymnastics typically invoked in many evolution accounts. Evolutionists contend that the Archaea, or the new archaeal phyla placed in the kingdom Protoarchaeota, holds the ancestor of the eukaryotes. The Archaea contain what are considered ancestral versions of signature systems involved with phagocytosis currently found in the eukaryotes. 31 It is contended that a wall-less organism of archaeal lineage accidentally engulfed an alpha-proteobacterium initiating the creation of eukaryotes.32,33

The initial endosymbiont subsequently evolved into an organelle, the mitochondrion, that membrane-bound organelle characteristic of eukaryotes and essential for energy generation. The plastids similarly are considered to have evolved through an endosymbiotic relationship, this time with a cyanobacterium. The ingestion of this bacterium was by a mitochondrion-containing eukaryote.34 More than 20 theories have been generated to account for the origin of eukaryotes from bacteria. This means that there is massive uncertainty about the most fruitful line of enquiry in which to engage. Perhaps understandably, some researchers have labelled the work of others as ‘entertaining fantasy’ or ‘research gone astray’. Nothing is settled.35,36 It is admitted that there is no direct evidence to support any of the possibilities suggested.37-39 This leaves the question of origins of circadian rhythms in the arena of speculation.

If the alpha-proteobacteria are considered as ancestors of the mitochondrion, it would be also logical to look at this group as contributing something to the development of a circadian clock in the eukaryotes. The results also have been disappointing; no evolutionary homology has been found. Selected purple bacteria (alpha-proteobacteria) do show periodic gene expression. In Rhodobacter sphaeroides, rhythmic gene expression has been found driven by the oscillatory protein KaiC. It appears that a KaiBC-based system is able to drive circadian-like rhythms in this organism, which shows a period of 20.5 hours in the transcription of the aidB gene.1 The situation is no better in a member of the group thought responsible for engulfing the alpha-proteobacterium. For example, in Haloferax volcanii (an archaeon), a KaiC-related system operates to enable a light-dark-dependent response (rhythmic) from a number of genes, but it fails to satisfy the full requirements to give it genuine circadian status. The genes (cirA to cirD) code for proteins that showed sequence similarities to the KaiC protein (28 to 55%) and also contain motifs characteristically found in KaiC proteins. When other haloarchaeal genera are considered, homology among the clock proteins is disappointingly low (25 to 30%).1,40

It is apparent, then, that the clock components are not conserved across the kingdoms. This has led to the conclusion that clocks seen in the different phylogenetic kingdoms arose separately.41 It is not even known how the simplest of cyanobacterial circadian clocks arose. Speculative schemes have been invented, but nothing rests on solid ground.42

Critical observations

The common features noted in circadian clocks, other than the points outlined by definition, are that they possess some type of oscillator which is responsive to environmental inputs and it delivers a variety of outputs. This means that a basic design is evident. On a deeper level, there are enormous differences seen among the kingdoms, with transcriptional-translation feedback loops characterizing the eukaryotes and post-translational circuitry the prokaryotes. However, both groups have feedback loops and post-translational mechanisms somewhere in the operational system. Again, on the broad-organizational level, design aspects are noted. At a theoretical modelling level, two basic design principles appear to exist, namely: a) well-defined phosphorylation states exist and are associated with rate constants that ensure unidirectional movement [phosphorylation (e.g. kinase) to dephosphorylation (e.g. phosphatase)], and b) oscillations of single molecules are synchronized by tight binding of enzyme by a substrate meaning that the enzyme is depleted before competing reactions occur.16

The transition from a cyanobacterial clock (simplest) to that of a photosynthesizing eukaryote (most complex) presents enormous challenges. The lack of clock component conservation across this divide has led some to conclude that the evolution of the clock in each major group occurred independently. However, no reasonable scenario has been constructed to account for these events. In addition, looking back billions of years, to when cyanobacteria are considered to have arisen, the day-length is thought to have varied from 11 hours to what is observed today, requiring further adaptation. 43 This undoubtedly would be explained by evolutionists by recourse to mutational changes, which have been found capable of altering (shortening or lengthening) the circadian rhythm length.44,45

Fitting the clock into the creation account

The biblical record has the green plants arising on Day 3 of creation. We suggest that the simplest (cyanobacterial) and most complex clocks were created in their respective living systems on that day. The archaea and bacteria (non-photosynthetic) possibly were created on Day 2. Light from the sun, as we know it, came on Day 4, providing the principle entrainment stimulus, light. On Days 5 and 6 the sea creatures, mammals (including humans) were created rounding out the picture. In this account there is a logical division among the eukaryotes. The most complex clock systems were created on Day 3 and the less complex on Days 5 and 6, with some design similarities observed. From an evolutionary viewpoint, the progression from a more complex to less complex organizational and functional clock system over time represents an anti-intuitive progression, as plants appeared before animals. However, this does not constitute a problem in the creation account for plants have the most varied operational arrangements in response to light. When considering animals with regard to other operational systems, such an analysis indicates that they outclass plants in operational complexity. Indeed, they have their own novel systems.

The 24-hour length of circadian clock cycles fits into the creation account. The Hebrew word for day is yom. It appears regularly in Genesis 1 (verses 5, 8, 13, 19, 23, 31) to describe what was accomplished on each day of creation. Whenever a definite number (e.g. first, second, etc.) is associated with the word ‘day’ in Hebrew literature, the time period is 24 hours.46 A strong argument cannot be made for the creation days being 24 hours in length by reference to the periodicity of circadian rhythms commonly observed today. This is on account of the observation that mutations may alter the circadian rhythm length.44,45 Nevertheless, it is observed readily that there is no contradiction between the biblical text and the periodicity of the rhythmic cycles we now observe. It constitutes an observation favouring belief in the Word of God.

We have noted already that some common design features are noted across all biological clocks. The specified complexity concept is also involved for the system must run repetitively to reflect compliance with the earth’s rotational cycles of 24 hours. Furthermore, all the parts contribute to the outcomes, in other words, functional coherence is observed. Such coherence cannot be explained in the absence of an intelligent agent being involved.47 The complexity observed in the so-called higher organisms indicates that they possess robustness,22 a feature particularly valuable post-Fall.

While in everyday life it is accepted that evidence of design and functional complexity is indicative of an intelligent Designer, this same observation is not readily admitted when scientists seek to explain origins in the natural world. In commenting on such a stand, it has been observed that if the designers of the Search for Extraterrestrial Intelligence (SETI) program took the same attitude, then there would be no purpose pursuing the project.48 This project represents a serious search for life elsewhere in the cosmos and initially the search is for narrow band radio signals from outer space. The existence of such signals or the detection of laser flashes from planets in the galaxy would be taken as proof of extraterrestrial life.49

The idea of design and a designer are powerful concepts that appeal to the Christian dedicated to believe in God’s revelations as did the apostle Paul. He said: “For since the creation of the world His [God’s] invisible attributes are clearly seen, being understood by the things that are made, even His eternal power and Godhead, so that they [those who do not believe in God] are without excuse” (Romans 1:20, NKJV). It should be noted that even Charles Darwin could not accept entirely the idea that the world we see is the result of blind chance or of necessity. Even for him some design was evident.50

Conclusions

Interpretation of the biblical text, using the historical grammatical approach, leaves a firm conviction that creation was accomplished in six literal, 24-hour days. This contrasts with all other ideas circulating today. The creation of the sun and moon and hence the dark/light cycle regulated by astronomical markers on Day 4 of Creation Week was momentous. This event was preceded (Day 3) by the creation of plants and followed by other living forms on Days 5 and 6. The ancient roots of the 24-hour dark/light cycle instituted at creation are believed to be reflected in the periodicity shown in the circadian rhythms found in almost all living things.

Elucidation of the biochemical events associated with circadian rhythms has been challenging even in unicellular organisms. Three proteins are involved in oscillator construction (post-translation oscillator) in simple organisms such as cyanobacteria, but in plants and mammals the cycles are intricate, and the circadian clocks are based on transcription-translation feedback loops. Nevertheless, there are basic design patterns that can be traced throughout all life forms. These involve both post-translation circuitry and stimulatory and inhibitory activities in feedback loops over a 24-hour period. In feedback loops, each gene produces a protein that repressed the next gene in the loop. In plants and mammals there are many proteins involved and the interactions are complex. We think that these design principles and the irreducible complexity shown in the simplest synthetic regulatory network confirms the reality of the creation account. The complexity of the cellular and biochemical events associated with circadian rhythms cannot readily be accounted for by a model of origins other than one involving an intelligent designer.

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  46. Nichol, F.D., Cottrell, R.E., Neufield, D.F. and Neuffer, J. (Eds.), The Seventh-day Adventist Bible Commentary, Review and Herald Publishing Association, Washington, DC, vol. 1, p. 53, 1953. Return to text.
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Inspiration from Creation
by Professor Stuart Burgess & Dominic Statham
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