In addition to energy-entropy alternation, the cell also employs biocycles to produce bioenergy/mass. Both of these processes can be viewed as strategies as they occur over time and serve a holistic purpose – cellular survival.
The Calvin cycle, i.e. the dark reaction of photosynthesis, is a superb example of a biocycle. Biocycles differ from familiar astronomical cycles in a variety of ways; transformative vs fixed content; external energy and assistance vs. self-contained; and deliberate, holistic purpose vs. random, atomistic reactions.
Biocycles can be understood as engines, as they transform external fuel into a useful product. This metaphor breaks down in that biocycles have transformative content, while engines have fixed content. These metaphorical parallels and differences are exhibited by the specifics of the Calvin cycle.
All engines require humans to design, manufacture and assemble the parts. Further these same humans must recognize the holistic purpose of the engine, e.g. remove water from coal mines. Applying this logic, biosystems must have had some kind of intelligence to both design/manufacture/assemble the parts and to recognize the holistic purpose of the biological machine.
Although metaphors are never exact, the engine metaphor is the best we have to understand biocycles. Although some might offer the conventional Material Dogma as an alternative, this outmoded paradigm falls impossibly short in many regards, e.g. holistic purpose. Although our engine metaphor implies intelligent design, do you have a better conceptual metaphor for understanding the holistic nature of biocycles?
Recap: Holistic Cellular Strategies vs. Atomistic Chemical Reactions
How Biocycles (Cellular Strategy #2) differ from Material Cycles
Biocycles & Intelligent Design?
Our exploration of cellular energy production started with strategies. We utilize the term ‘strategy’ to emphasize the holistic nature of the process. This deliberate holistic focus simultaneously deemphasizes the atomistic chemical nature of cellular energy production.
An atomistic focus has been deliberately adopted almost universally by bioscientists. Why? To draw our attention away from Life’s holistic behavior. Why? The conventional Material Paradigm can’t deal with holistic systems. Why? Material systems are always atomistic, in that the parts determine the nature of the whole, Atomistic (reductionist) logic cannot be employed to understand holistic systems, such as the cell.
Cells, and by extension all living systems, deliberately interact with the ongoing flow of environmental information. This interaction is holistic in that the purpose is the survival of a Being with dynamic content (not fixed). Rather than interact with information, molecules react immediately to stimuli. This material reaction is atomistic as it does not take the whole into account, even though it might affect the whole.
Atomistic, material systems certainly don’t employ deliberate strategies. In contrast, holistic living systems such as cells employ multiple step strategies to store energy in order to survive as a unit. One such cellular strategy is the alternation of energy and entropy. Glycolysis, a process employed by all cells, utilizes this strategy to double the initial investment of bioenergy.
A second cellular energy strategy is the employment of biocycles. The cell employs the biocycle strategy in the two primary processes of cellular energy production – photosynthesis and cellular respiration. The Krebs cycle, an important stage in cellular respiration, is one such biocycle. We will examine this process in a subsequent chapter. The Calvin cycle, a crucial stage in photosynthesis, is another example of a biocycle.
Why are biocycles, such as the Calvin cycle, special? How do they differ from more familiar material cycles? Read on for some answers.
Reviewing: In the light reaction of photosynthesis, the cell transfers solar energy to an electron. The subsequent dark reaction of photosynthesis employs the solar energy stored in the electron to generate G3P, a high energy biomolecule that the cell can subsequently convert into biomass or bioenergy. The dark reaction is also called the Calvin cycle, our first biocycle. Rather than trivial, this cyclic process is essential for the survival of all multicellular life forms, such as ourselves.
The Calvin cycle is not like other cycles you have met. In astronomical cycles: the Moon revolves about the Earth; the Earth revolves about the Sun; and the Sun revolves about our galaxy, the Milky Way. In each of these cases, the content remains the same and the process requires no outside assistance. Plus, these revolutions have no purpose (unless you believe in astrology.)
Due to the Earth’s revolution on its axis, day turns into night which turns into day. Again content remains the same, no assistance is required and the revolution’s serve no purpose (unless you believe in the Gaia hypothesis).
In the Earth’s water cycle: from high in the mountains, water flows down rivers into oceans. Here it evaporates into clouds. These clouds rain down on the mountains – replenishing the rivers, which run into the ocean. Although the phase changes from liquid to gas (even solid in some scenarios), the molecular content of the water remains the same. Plus the phase changes require no material assistance and have no holistic purpose.
In each of these familiar cycles, the content remains the same. Conversely, the molecular content changes with each step in the Calvin cycle. In each step, one molecule is transformed into another different molecule.
In addition to content, the energy and forces that drive our familiar cycles and the Calvin cycle are qualitatively different.
Each phase in the Calvin cycle is an uphill reaction in that each requires external energy to drive the process. Where does this energy come from? Not from the erratic random collisions of atoms and molecules. Not from naturally occurring forces, e.g. gravity, an eternal force of nature. Rather the preceding light reaction methodically transforms sunlight into high energy biomolecules. These special particles provide the bioenergy that drive the three phases of the Calvin cycle.
Happening ‘naturally’ due to gravitational forces, planetary revolutions require no added energy. They are all downhill. The water cycle requires solar energy to transform it into clouds, but afterwards it is all downhill – literally.
None of these natural processes require special ingredients and intermediaries to ensure that the cycle proceed smoothly. Planetary revolutions, star and galaxy formation, the water and glacier cycles, atom and molecule generation, all happen randomly/naturally without any special helpers.
In contrast, the Calvin cycle requires outside help from special ingredients in each of its many steps. In order to transform molecules into a succession of entirely different molecules in a series of chemical reactions, the Calvin cycle requires unique biomolecules (enzymes) to ensure that the reactions occur at life speed – not too slow, not too fast, just right. Indeed, many of the cell’s metabolic pathways require the external assistance of enzymes in order to perform their magic.
The cell produces these special biomolecules internally – within its myriad metabolic pathways. None of these special ingredients is farmed out to subsidiaries for production. All of this occurs within the cell.
There is no material cycle, whether astronomical, earth-based or resource-driven, that requires special ingredients that are deliberately produced within the system for this specific purpose. However, this is standard practice for every cell on the whole planet. Nothing special, if you happen to be a cell. Sorry to be repetitive, but this biosynthesis of complex high energy molecules by the microscopic cell continues to astound me!
So the Calvin cycle is not just any old cycle. Its content changes molecular form each step along the way; each step requires external energy; and each requires a special ingredient to ensure that the reactions occur in a timely fashion. In the familiar material cycles that we focused upon, molecular content remains the same; energy is supplied by natural forces rather than specifically created; and no special ingredients are required to drive the cycle.
Although dynamic content, uphill reactions, and external assistance are unique to these cyclic cellular processes, there is another factor that really sets biocycles apart from material cycles. Biocycles such as the Calvin cycle have an express purpose – to serve the holistic needs of the cell. The sole purpose of the Calvin cycle is to produce the G3P molecule, which the cell employs to produce biomass/energy. Without the Calvin cycle, nucleated cells such as ours could not survive. As such, the Calvin cycle derives its meaning in relationship to the cell. In contrast, the only meaning that material cycles have is that with which we invest them. Atoms and molecules, planets and galaxies only serve themselves. As the building blocks of our material universe, they are independent of the whole.
Having shown how exceptional biocycles are, let us now focus upon specifics of the Calvin cycle.
The Calvin cycle has three phases: 1) carbon capture, 2) creation of G3P (the building block molecule of biomass and bioenergy) and 3) the regeneration of the molecules required to start the cycle again. Each phase has a distinct purpose – serving the energy needs of the cell.
In the Calvin cycle, a 5-carbon molecule (RuBP) could be said to initiate the cycle. (As the cycle is ongoing, it really has no beginning or end.) In the first stage, three carbon dioxide molecules from the outside interact with 3 of these 5-carbon molecule to generate three 6-carbon molecules.
This stage is called carbon capture, as the 3 carbon atoms that enter the system eventually become the foundation of all the biomolecules necessary for Life, both bioenergy and biomass. This incredibly significant moment is not naturally random, but is instead deliberately strategic. This molecular transformation occurs only with the aid of Rubisco, the most abundant and one of the most complicated enzymes on the planet.
And where did this incredibly complex molecule that is contained in virtually every plant arise? Spontaneously, from random collisions of atoms and molecules? Not! Rather, as might be expected, each cellular factory synthesizes this mega-molecule in its microscopic metabolic pathways.
Now that the external carbon derived from the air is in the system, the real magic is complete. The other stages, while significant, complicated and uphill, are standard metabolic fare. Enzymes with the assistance of bioenergy derived from the previous ‘light reaction’ catalyze the transformation of biomolecules from one form into another.
Due to their unstable high energy state, our three 6-carbon molecules are ripe. After capturing the carbon atom, the super-enzyme rubisco splits the three 6-carbon molecules into six 3-carbon molecules.
It is now that the solar energy that was transmitted to the electrons and then to the biomolecules in the first stage of photosynthesis comes in handy. With the energy and phosphate groups from 6 ATP molecules combined with the energy from 6 NADPH molecules, these six 3-carbon molecules are stepped up in energy to an even higher level of biocomplexity – some say the highest. These six 3-carbon molecules are transformed into six G3P molecules, the building block molecules of bioenergy and biomass.
At this point in the cycle, five of these G3P molecules continue on in the Calvin cycle. With the assistance of some ATP molecules that are charged with solar energy and, of course, some enzymes, these five 3-carbon molecules are transformed into the three 5-carbon molecules that initiated the Calvin cycle.
And the Calvin cycle continues. Carbon capture occurs with the aid of Rubisco, and so on and so forth. Rather than unique or unusual, this magnificent cyclic process occurs, according to some estimates, about three times every second in every plant cell on earth.
As mentioned, the second stage of the Calvin cycle produces 6 G3P molecules. Five of these stay in the cycle. Only one leaves. This G3P molecule could be considered the product of the Calvin cycle. If it enters the glycolytic pathway, it is converted into bioenergy in the form of charged ATP molecules. If it enters other pathways, it can be transformed into glucose, a form of biomass and a more stable energy source, or even glycogen, an even more durable form of biomass. Recall biomass is stored bioenergy.
What is the difference between biocycles and other biological processes? The cell’s overall energy production processes, i.e. glycolysis, photosynthesis, and cellular respiration, all start with one molecule and end with another. In contrast, both the Krebs cycle and the Calvin cycle start with one molecule and end with the same molecule, so that the process can start anew. Put another way, the molecule that initiates the process is transformed into a different molecule in each stage before returning to its initial state at the end of the cycle. None of the intermediate molecules are exhausted, i.e. need to be replenished.
For example, only 3 carbon atoms enter the Calvin cycle via 3 carbon dioxide molecules and only 3 carbon atoms leave the cycle via G3P. In other words, there are 15 carbon atoms at the beginning and end of the cycle. Furthermore, it is the same with every other atom in the system. While the molecular content changes, the atomic content remains intact.
Questions naturally arise as to origination of this mysterious process. As the cycle is self-sustaining, where did both RuBP (the first 5-carbon molecule that initiates the cycle) and Rubisco (the enzyme that enables carbon capture) originate? As each of the stages only has meaning in relationship to the whole, where did the individual enzymes that catalyze each chemical reaction arise? As the Calvin cycle’s dark reaction only has meaning and functionality in terms of the prior light reaction of photosynthesis, how did it come to be without the bioenergy supplied by this stage? As the G3P molecule only has meaning regards the survival and energy needs of holistic living systems, how could the linear atomistic reactions of material systems have resulted in the creation of this microscopic particle that is the basis of both biomass and bioenergy? Lacking both a temporal and holistic sense, how could the random interactions of minute particles accidentally come up with these ongoing, deliberate strategies that are designed to enable the survival of a holistic Being?
Could it be that a divine source with both a holistic and temporal sense somehow deliberately arranged some divine coincidences to facilitate Life?
Cells have a variety of strategies for producing energy and in a larger sense maintaining homeostasis. The first strategy we discussed was the alternation of energy and entropy. The cell spends potential energy stored in ATP molecules to do work, then relies upon entropy to complete the process. Glycolysis’ 10 step process epitomizes this strategy.
Biocycles, endless cyclic processes, are yet another type of strategy that cells employ to generate energy. The carbon cycle, Krebs cycle and Calvin cycle are all examples of this strategy. Each of these cycles has some common features. In each case, the end product is also the beginning of the next cycle. Indeed due to the endless and ongoing nature of the cycle, it is impossible to really identify the beginning and end.
In each case, an ingredient enters the biocycle from outside the system. This substance could be considered the system’s fuel. For instance, pyruvate enters the Krebs cycle and carbon dioxide enters the Calvin cycle, and more generally the carbon cycle of photosynthesis/cellular respiration (to be dealt with later).
From this fuel, each of the cycles produce something that is useful to the cell. The Krebs cycle charges the molecules that drive chemiosmosis; the Calvin cycle produces G3P; and the greater carbon cycle produces bioenergy/mass.
Finally, and maybe most importantly, the components that comprise these biocycles are not used up. They are not fuel. Although the biomolecules that enable the cyclic processes go through transformations from one form to another, the basic elements remain the same; they are not depleted. For instance, ATP gives up its potential energy to become ADP and then ADP is charged to become ATP. In similar fashion, the electron transport molecules (NAD and FADH) are charged, then release the charge, and then are charged again. Synthesized elsewhere, these biomolecules alternate between one state and another.
This same analysis holds true for all the biomolecules in these cycles. They go through the same molecular transformation over and over again with each cycle. Yet they are not produced by the cycle. As with the ADP/ATP alternation and the electron transport molecules, they are synthesized in other metabolic pathways.
Because fuel is transformed into a useful product by unchanging elements, these biocycles have been likened to an engine. For instance, a car’s engine transforms gasoline into useful motion, but remains relatively unchanged. While the engine metaphor is a useful way of understanding biocycles, it can easily provide a false sense of equivalence.
The engine metaphor breaks down in the details, as all metaphors do. The engine’s components remain intact. Indeed except for wear and tear, their molecules are virtually unchanged from the beginning to the end. For instance, the content of the car’s carburetor remains constant. In contrast, the biomolecules in the biocycles are regularly transformed from one state to another. Indeed many of the major biomolecules change into a new form in each stage.
In summary, the cell employs two types of strategies to produce energy: 1) the alternation of energy and entropy and 2) the biocycle. Both types of strategy produce a product that is useful to the cell and both strategies take advantage of time. Further rather than relying on the random collision of molecules, both types of strategy have distinct steps that must occur in a timely fashion in order to fulfill a distinct purpose.
Matter does not have these capabilities, while Life’s ID system does.
To enhance understanding, humans regularly employ conceptual metaphors. To better conceptualize the operation of cellular biocycles, we employ the metaphor of an engine. We have all experienced an engine, for instance cars and bikes. In each case, fuel or energy enters the system from the outside. The engine or biocycle then converts this fuel/energy into a form that is useful to the system, e.g. work or product. A car’s engine converts gasoline into useful motion and the Calvin cycle converts carbon dioxide into biomolecules that are useful to the cell.
We mentioned a significant metaphorical breakdown. The contents of the components in our engines remained fixed, while the cellular components are transformed from one molecular form into another. Despite this discrepancy in the internal logic of the two types of systems, the engine metaphor still remains useful.
In both cases, the parts are manufactured/synthesized elsewhere. After manufacture, these parts are then transported and assembled where they are needed. For instance, a bike’s wheels, tires and frame are first manufactured, then transported and finally assembled into a workable machine that can transport a rider. Similarly, the cell first synthesizes enzymes, then moves them to where they are needed, and then finally embeds them in the mitochondria’s membrane where they can perform useful work.
So far so good in terms of the engine metaphor. Now comes the leap. Every engine ever made required a human to design the parts and the machine. For instance, the multiple stage engines that drew water from coalmines in the 18th and 19th century required ingenious humans to first conceptualize, then manufacture and finally assemble the parts into a workable machine. These earliest engines had to be efficient and economical enough to replace the horses that were performing the task. James Watt, an early inventor and entrepreneur, employed the term horsepower to indicate the number of horses that these early machines could economically replace.
Rather than the accidental random collisions of molecules, humans like James Watt deliberately designed and produced these multi-stage engines that replaced the horse. Indeed, the potential riches derived from designing a more efficient engine motivated these early inventors to focus their Attention upon invention. Although some of the innovations might have been accidental or random, the inventor still had to deliberately incorporate them into his design. The intentional manipulation of events permeates this inventive process.
So what about these engines that produce cellular energy? These biocycles are arguably far more complex than our machines, in that their components are regularly changing molecular identity. Our engines require a designer. Why not these biocycles? The arbitrary random collisions of molecules can’t produce even the simplest machine no matter how much time they have.
Further, even the most rudimentary engine requires someone who recognizes the potential use. A car is useless to a giraffe. So these biocycles require both a designer and some kind of being that recognizes the utility and then can put it into practice.
Of course, all these predications are based upon metaphorical logic. Simply put, the logic of the machine approximates the logic of the biocycle. This conceptual metaphor has enabled us to have a better understanding of the biocycle’s logic.
Yet we know that metaphors are never exact, always approximate. Indeed, we have already exposed a discrepancy – fixed vs transformative content. Despite the imprecision, this is all we have. And if the metaphor holds, intelligent design is the implication.
Of course, the scientific community always falls back on their material metaphor to avoid the dreaded intelligent design. Clinging to this misguided model like a security blanket, they ignore its impotency before Life’s holism. We have already exposed many fatal flaws in the random collision approach that relies upon the emergent properties of self-organizing matter. The cell’s irreducible complexity, which includes biocycles as an indispensable feature, is indisputable. The mutual dependency associated with this scientific fact alone confutes the conventional Material Dogma.
Rather than attached to a deliberate higher power, we’re open for options. Human understanding is limited by our time and neurology. Indeed, we cannot really conceptualize the impossibly paradoxical Subatomic Realm. But can you think of another way of conceptualizing biocycles that does not involve intelligent design?