Created: September 9, 2015
Revised:Synopsis Sept 2017  

The Creation Narrative of Science and the Bible

Dr. David C. Bossard

Dr. David C. Bossard
Biographical Information

Photosynthesis and Carbon Fixing
How it works.

Life cannot exist without an energy input from outside itself. That could be organic food (products of earlier life), energy from sunlight, thermal vents, etc. Obviously organic food is not an option for the very early species, which appear in the geologic record at almost earliest possible moment after the earth had cooled to a "livable" temperature, at around 3.8 Ga (Billion Years Ago)—a very hot temperature, perhaps about that of pasteurization (140-150°F)M.50.

The organic carbon found as early as 3.8 Ga, and the fossils of what appear to be cyanobacteria (or their ancestors) around 3.45 Ga indicate that photosynthesis, harvesting of energy from sunlight, appeared with the first life, or very soon thereafter.M.51 

Photosynthesis is an incredibly elaborate process, and the basic parts of it are essentially the same for all photosynthetic life. The cyanobacteria conduct photosynthesis in folded membranes called thylakoids ("light reaction" in the following figure). Plants conduct photosynthesis in Chloroplasts as show in the Figure.M.52  

A number of complex molecules, some actually nano-sized motors, are involved in photosynthesis. There are two stages: the light reaction which harvests energy from light, and the dark reaction (Calvin Cycle in the following diagram), which uses the products of the light process to fix carbon and make sugars. The dark reaction does not harvest light but exchanges products with the light reaction.


The following (deceptively simple) chemical equation describes the action of photosynthesis:

6H2O+6CO2+light energy -> C6H12O6+6O2
Water + Carbon dioxide + light energy -> sugar + (waste) oxygen.

The Light Reaction.

The light process centers around chlorophyll: molecules that harvest light with the help of a central magnesium atom. There are two forms of chlorophyll which work cooperatively but have, remarkably, opposite characteristics—one is a strong oxidizer, and the other is a strong reducer—each the best known design for its particular task to be found in all of nature.

Photosystem II, involving P680 Chlorophyll: absorbs yellow (680 nm) light. This is the strongest known biological oxidizer. It oxidizes water to produce protons (H+ = P) and  oxygen (O2) as a waste product in the Oxygen-evolving complex. It is "II" because it was discovered after Photosystem I. The protons are used in the manufacture of ATP, the universal "energy battery" used, in particular, in the dark process. A summary of its action is:

H2O + light energy ->  2 H+ + O2
water + light energy -> protons + oxygen.

Photosystem I, involving chlorophyll P700: absorbs orange (700 nm) light. This is the strongest known biological reducer. It uses light energy to prepare a precursor molecule NADPH for sugar production in the dark process.

The protons of Photosystem II supply protons (H+) to Photosystem I to make NADPH, and also propel a marvelous and complex rotary proton nanomotor, ATP synthase, which prepares ATPM.53   (see figure).



ATP Synthase

The Dark Reaction.

The dark reaction  fixes carbon and then uses it to form glucose, C6H12O6, used by the cell to form starch, amino acids and other sugars. The following remark emphasizes the importance of carbon fixing.

"Carbon is essential to life. All of our molecular machines are built around a central scaffolding of organic carbon. Unfortunately, carbon in the earth and atmosphere is locked in highly oxidized forms, such as carbonate minerals and carbon dioxide gas. In order to be useful, this oxidized carbon must be "fixed" into more organic forms, rich in carbon-carbon bonds and decorated with hydrogen atoms.M.54

This is done by a complex motor molecule, RuBisCO. It is the most common protein on earth—about half of all the protein. The RuBisCO molecule is large (consisting of two subunits),  very slow (it can fix about 3 CO2 molecules per second) and very inefficient, because it spends about 20% of its time "fixing" oxygen instead of carbon: "a wasteful process"M.55 called photorespirationM.56.  One author called the molecule "dim-witted."  Nonetheless, despite many billions spent seeking an improved RuBisCO, no practical substitute has been found. The RuBisCO active site uses a Magnesium atomM.57  to perform its function. The overall reaction can be summarized as:

CO2 + H2O + ATP → CH2O + O2
carbon dioxide + water + ATP -> sugar (fragment) + oxygen + ADP + P+++

where ATP is the energy "battery" with three phosphates, one of which is released generating energy, ADP and a phosphate ion. This is repeated three times in the Calvin cycle.

RuBisCO discriminates against the isotope 13C, preferring the slightly lower mass of 12C. This arises due to slight differences in kinematics and binding energy in the CO2 molecule. Thus organic carbon is slightly deficient in 13C compared with inorganic carbon.

[*fn]M.50 Some scientists believe that the first life was extremophiles such as live near thermal vents in the oceans. This would move the possible time of the first life even earlier, around the boiling point of water. Personally I think that extremophiles are a later development. See, for example, Cell Biology, " Archaea are microbes that are more closely related to Eukaryotic cells than they are to the Bacteria". The Archaean ribosomes appear to be closer to Eukaryotes (much later) than to bacteria—see Margulis & Chapman, Kingdoms and Domains (2009), Figure B-3, "Ribosome morphology".

[*fn]M.51 Haselkorn, Koonin, et al, The cyanobacterial genome core and the origin of photosynthesis (PNAS, 2006). They assert that the earliest cyanobacteria already had both the light and Calvin processes in place. These are two very complex and subtly linked processes and involve many specialized molecules working together. Processes and complex molecular motors accompanying photosynthesis: energy storage (ATPase), and carbon fixing (RuBisCO) to make sugars. Nitrogen fixing (Nitrogenase) also accompanied photosynthesis —by necessity—but it is a separate process. According to these authors, "These are such complex biological processes, that the complexity and early appearance on earth seems to indicate planning and design."

[*fn]M.52 In Eukaryotes, photosynthesis takes place in the chloroplast. In bacteria, the thylakoids, like the DNA itself, is located in the undifferentiated general cell contents.

[*fn]M.53 See an ATP Synthase animation by Donald Nicholson (Leeds  University) and a more detailed molecular view by John Walker (Cambridge). See the description from Davidson College. See also the article on ATP Synthase from, which calls it "the smallest rotary motor in the world. ... ATP synthase was one of the first enzymes because it is absolutely necessary for many of the organisms that are thought to have existed on the primitive earth. All of the bacteria that oxidize non-organic chemicals to obtain energy use ATP synthase to make ATP." The molecule is constructed from six subunits. The first recognized nanomotor, the bacterial flagellum, was offered to an incredulous scientific world in the 1980s. At first the discovery of this motor was met with great skepticism; it was thought that the flagellum did not rotate but simply whipped back and forth. The proof came when a scientist found a way to glue the flagellum to a glass slide, and when this happened, the bacterium spun around the flagellum. Since then literally thousands of nanomotors have been identified.

[*fn]M.54 Buick, R. "Earliest Evidence for Life on Earth" Bulletin of the American Astronomical Society, Vol. 34, p.12 (2002).

[*fn]M.55 Wasteful, because the cell must expend time and energy to reverse this error.

[*fn]M.56  To fix carbon, food, energy: fix Rubisco (Biofuels Digest, 2010).

[*fn]M.57 Occasionally Vanadium is known to substitute for the Magnesium atom.

M.58 [*fn]M.58 Note for M.58

M.59 [*fn]M.59 Note for M.59

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