An international team of scientists has published an article in Nature magazine, suggesting that oxygen began accumulating in the atmosphere at least three billion years ago. The team’s findings raise a troubling question for Darwinian evolutionists: how did the exquisitely complex metabolism of oxygenic photosynthesis arise so soon after the dawn of life?
The team arrived at its conclusions by studying the ratios of two isotopes of chromium – chromium-52 and chromium-53 – in the world’s oldest soils: former soils preserved by burial under rocks in Kwazulu-Natal Province, South Africa, dating back to 2.95 billion years before the present. Because chromium-53 is slightly more soluble when oxidized than chromium-52, the team was able to infer the composition of oxygen in the Earth’s early atmosphere, by measuring the relative abundances of the two isotopes. A BBC report by Jonathan Amos explains how the team arrived at its conclusion:
…[O]ver time, soils that have been oxidised should become depleted in chromium-53 as rain water washes away these atoms; and, conversely, sea sediments, where the products of weathering eventually end up, should become enriched in chromium-53.
The team made precisely this observation in Kwazulu-Natal, in rocks that represented both ends of the process – the soils and the sea sediments.
The conclusion is that the ancient soils would have been exposed to an atmosphere that contained 0.03% of the oxygen it does now; about one-10,000th of the present level.
An oxygen concentration of 0.03% might not sound like much, but it’s at least 10 times higher than most scientists had previously expected. As the Nature article explains, the new finding radically revises the old picture:
It is widely assumed that atmospheric oxygen concentrations remained persistently low (less than 10^−5 [0.00001] times present levels) for about the first 2 billion years of Earth’s history. The first long-term oxygenation of the atmosphere is thought to have taken place around 2.3 billion years ago, during the Great Oxidation Event. Geochemical indications of transient atmospheric oxygenation, however, date back to 2.6–2.7 billion years ago… Overall, our findings suggest that there were appreciable levels of atmospheric oxygen about 3 billion years ago, more than 600 million years before the Great Oxidation Event and some 300–400 million years earlier than previous indications for Earth surface oxygenation. (Square brackets mine – VJT.)
Evolution of the gaps
The BBC report carried the following comment from the lead author of the Nature article, which is remarkable for its Darwinian doublespeak:
“Oxygenic photosynthesis is a very complicated metabolism and it makes sense that the evolution of such a metabolism would take perhaps two billion years – that we might not see its manifestation until the Great Oxidation Event. But now that we see oxygen much earlier in the atmosphere, it tells us that even really complex metabolisms can evolve very fast,” said team-member Dr Sean Crowe from the University of British Columbia, Canada. (Emphases mine – VJT.)
Let’s see. Oxygenic photosynthesis appeared much sooner than scientists thought, so evolution must be capable of creating complex mechanisms very quickly. How very convenient. The term “evolution of the gaps” was aptly coined for this kind of reasoning.
And before anyone tells me that life had already existed for some 800 million years before the first appearance of oxygenic photosynthesis 3 billion years ago, they might like to have a look at an article by Roger Buick, entitled, When did oxygenic photosynthesis evolve? (Philosophical Transactions of the Royal Society B, 27 August 2008, vol. 363, no. 1504, pp. 2731-2743), which tentatively concludes that 3.8 billion-year-old U–Th–Pb isotopes found in metasomatized and metamorphosed turbidites (a type of layered sedimentary rock) in Isua, Greenland, “perhaps represent the earliest evidence of oxygenic photosynthesis.” If Buick is correct here, then oxygenic photosynthesis goes right back to the very dawn of life. How would Dr. Crowe explain that, I wonder? (To be fair, I should mention that Dr. Steve Drury, of the Open University, reaches a somewhat different conclusion. In a 2013 post, he argues that the 3.8 billion-year-old rocks found at Isua, Greenland, do indeed indicate the presence of bacteria on the primordial Earth at that time. However, in his view, “the most likely bacterial type involved at Isua may have been a photosynthesiser, but not of the kind that releases elemental oxygen instead transferring it from water to combine directly with the ions of iron that its photosynthesis had oxidised.” Dr. Drury may well be right here, although I should point out that the occurrence of even this simpler kind of photosynthesis at 3.8 billion years ago is surprising enough: photosynthesis of any sort requires the co-operation of several proteins, as we’ll see below.)
Oxygenic photosynthesis: what’s all the fuss about?
“What is oxygenic photosynthesis, anyway?” I hear you ask. Good question. When I studied photosynthesis in junior high school, it was presented as a simple chemical equation:
6 CO2 + 6 H2O -> C6H12O6 + 6 O2
(Carbon dioxide and water produce glucose and oxygen, in the presence of light.)
It never occurred to me to wonder exactly how this process of molecular rearrangement took place, and I certainly never imagined that it had anything to do with proteins.
Let’s go back to basics. As I’m not a chemist, I intend to keep this exposition as light and non-technical as possible, and let the pictures do the talking.
Photosynthesis in plants. The carbohydrates produced are either stored in the plant, or used by it. Courtesy of Wikipedia.
The term photosynthesis refers to a living organism’s ability to make food directly from carbon dioxide and water, using energy from light. In most bacteria, light energy is captured and stored as chemical energy in the form of a molecule known as ATP, without the production of oxygen. This process is known as anoxygenic photosynthesis. But in cyanobacteria (or blue-green bacteria), plants and algae, photosynthesis releases oxygen. This process is called oxygenic photosynthesis, and it’s a more complex process.
The Wikipedia article on photosynthesis provides a handy overview:
Photosynthesis occurs in two stages. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide…
Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by proteins called reaction centres that contain green chlorophyll pigments. In plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances such as water, producing oxygen gas. Furthermore, two further compounds are generated: reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the “energy currency” of cells.
In plants, algae and cyanobacteria, sugars are produced by a subsequent sequence of light-independent reactions called the Calvin cycle… (Emphases mine – VJT.)
Even the simpler version of photosynthesis is impressive enough
Even the simpler version of photosynthesis (anoxygenic photosynthesis) presupposes the existence of a suite of proteins. Here, for instance, is how Wikipedia describes photosynthesis in green-sulfur bacteria:
Photosynthesis is achieved using bacteriochlorophyll (BChl) c, d, or e, in addition to BChl a and chlorophyll a, in chlorosomes attached to the membrane. They use sulfide ions, hydrogen or ferrous iron as an electron donor and the process is mediated by the type I reaction centre and Fenna-Matthews-Olson complex.
A photosynthetic reaction center, for those who are wondering, is “a complex of several proteins, pigments and other co-factors assembled together to execute the primary energy conversion reactions of photosynthesis” [emphasis mine – VJT]. (Co-factors are light-absorbing molecules.) Here’s what one looks like, in a humble bacterium:
A photosynthetic reaction centre inside a bacterium. Courtesy of the Protein Data Bank (authors Roszak, A.W., Howard, T.D., Southall, J., Gardiner, A.T., Law, C.J., Isaacs, N.W., Cogdell, R.J.) and Wikipedia.
And what about that Fenna-Matthews-Olson complex? It’s a pigment-protein complex (PPC) found in green sulfur bacteria, and it looks like this:
The Fenna-Matthews-Olson complex, found in green sulfur bacteria, is composed of three identical parts, called monomers. Each monomer contains several bacteriochlorophyll A molecules (depicted in green), a central magnesium atom (depicted in red), and a protein scaffolding (depicted in gray). The three monomers look rather like taco burgers, except that they’re filled with bacteriochlorophylls. Courtesy of the Protein Data Bank (www.pdb.org), Julian Adolphs and Wikipedia.
By the way, did I mention that the Fenna-Matthews-Olson complex is the simplest protein pigment complex appearing in nature?
I’ve said enough about the simpler version of photosynthesis. Now let’s talk about oxygenic photosynthesis.
Oxygenic photosynthesis: a staggeringly complex process
Photomicrograph of cyanobacteria, Cylindrospermum sp. Courtesy of Matthew Parker and Wikipedia.
Cyanobacteria (pictured above), also known as blue-green bacteria, are believed to have been the earliest organisms to engage in oxygenic photosynthesis, as plants and algae do. Under aerobic conditions, cyanobacteria are capable of performing the process of water-oxidizing photosynthesis by coupling the activity of two protein complexes, known as photosystem (PS) II and I, in a chain of events known as the Z-scheme. These protein complexes are located in the thylakoid (“pouch-like”) membrane of plants, algae, and cyanobacteria. The diagrams below illustrate what’s going on. First, here’s a schematic diagram, showing what a humble cyanobacterium looks like on the inside. The thykaloid membrane is shown in the diagram:
Diagram of a cyanobacterium. Courtesy of Kelvinsong and Wikipedia.
As we noted earlier, photosynthesis occurs in two stages: first, a light-dependent stage and then, a light-independent stage. Here’s what the first stage looks like:
Light-dependent reactions of photosynthesis at the thylakoid membrane. Courtesy of Tameeria and Wikipedia.
A photosystem begins photosynthesis by receiving light energy and then converting it to chemical energy. Perhaps you’re wondering what the molecules labeled Photosystem (PS) II and Photosystem (PS) I, actually look like. Here’s a diagram of a monomer of Photosystem (PS) II, as it occurs in cyanobacteria:
Photosystem II, as found in in cyanobacteria. Monomer, PDB 2AXT. Courtesy of Curtis Neveu and Wikipedia.
I wrote above that I was going to let the pictures do the talking. What hypothesis regarding origins does the picture above suggest to you? Be honest!
Here’s a brief description from Wikipedia of the role played by Photosystem II:
Photosystem II … is the first protein complex in the light-dependent reactions… The enzyme captures photons of light to energize electrons that are then transferred through a variety of coenzymes and cofactors to reduce plastoquinone to plastoquinol. The energized electrons are replaced by oxidizing water to form hydrogen ions and molecular oxygen. By obtaining these electrons from water, photosystem II provides the electrons for all of photosynthesis to occur.
And what does science have to say regarding the origin of Photosystem II? Here’s an excerpt from an Origins blog post titled, Seeking Microbial Missing Links by Mitch Leslie in Science magazine (April 1, 2009):
Bacteria are the Thomas Edisons of metabolism. They have “invented” myriad biochemical pathways that enable them to eke out a living from substrates as diverse as the oils on your skin, the tiny amounts of carbon monoxide in the atmosphere, and the hydrogen sulfide spewed by deep-sea volcanic vents. That metabolic diversity might include photosynthetic intermediates, scientists argue.
Researchers hope that such microbes will help them determine how early cells assembled the photosynthetic machinery, which involves more than 100 proteins working in concert to absorb light and make sugars. One of the most contentious questions in the field, as discussed in a recent Origins essay, is the origin of the photosystems, the molecular clusters that contain chlorophyll and other light-capturing proteins. Photosystems come in two flavors, I and II. Plants, algae, and primitive cyanobacteria all have both photosystems — and need both to exploit light energy. But other bacteria have only one molecular cluster — what scientists think are the ancestors of photosystem I or photosystem II. Microbial missing links might shed light on how the ancestors of today’s cyanobacteria ended up with two photosystems.
So far, researchers haven’t pinned down any of these missing links. But they take heart from a 2007 paper by microbial physiologist Donald Bryant of Pennsylvania State University, University Park, and colleagues that identified a new solar-powered bacterium… The bacterium isn’t photosynthetic. It has the “photo” part down, absorbing light energy with chlorophyll to make the ATP necessary for living. But it hasn’t mastered “synthesis.” Instead of using carbon dioxide to manufacture sugars, it depends on other bacteria for its carbon needs.
Doesn’t sound very promising, does it? Especially when you have to account for the origin of more than 100 proteins, and explain how they came to work together in concert!
A more recent paper by James P. Allen et al., titled, Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers (PNAS February 14, 2012 vol. 109 no. 7 2314-2318) argues that the complex manganese-calcium cluster needed to perform the reactions that oxidize water could have been built up gradually:
These results provide insight into the evolution from anaerobic to oxygenic photosynthesis. The core cofactors and subunits of photosystem II and the bacterial reaction center have similar three-dimensional structures (4, 23), with the D1 and D2 subunits of photosystem II and the L and M subunits of bacterial reaction centers being derived from a common ancestor. The evolutionary transition from primitive anaerobic phototrophs to organisms capable of oxygenic photosynthesis is thought to have triggered the great oxidation event approximately 2.4 Gyr [2400 million years – VJT] ago, in which molecular oxygen emerged as a significant constituent of Earth’s atmosphere (24–29). This transition would have required the development of a highly oxidizing complex with a Mn [manganese – VJT] cluster capable of water oxidation. Creation of a highly oxidizing protein complex could have been achieved through a combination of altered interactions between the bacteriochlorophyll dimer and the surrounding protein as well as the incorporation of more highly oxidizing tetrapyrroles, such as chlorophyll d (29–31)…
Leaving aside the fact that the appearance of oxygenic photosynthesis is now believed to have taken place at least three billion years ago, and not 2.4 billion years ago as the authors suggest, it seems to me that the authors have ignored the main problem: where did the various proteins that make up Photosystem II come from in the first place?
Regarding proteins, all we are told is that two proteins at the core of photosystem II, called D1 and D2, are homologous, and that they’re similar to “the L and M subunits of bacterial reaction centers,” suggesting a common ancestry. I have grown very wary of claims like these, so I decided to do a little fishing. I came across a paper by Jyoti Sharma et al. Primary Structure Characterization of the Photosystem II D1 and D2 Subunits (Journal of Biological Chemistry, 1997, 272:33158-33166, doi: 10.1074/jbc.272.52.33158). On page 33161, Figure 3 shows the protein sequence of the D1 subunit in photosystem II. On page 33164, Figure 6 shows the protein sequence of the D2 subunit in photosystem II. I would invite the reader to flip backwards and forwards between the two pages, examining the two proteins carefully. Despite the existence of broad similarities between the two proteins, there are also a large number of differences. That’s important, because recent research by Douglas and Ann Gauger (see this video) suggests that there’s a limit to how many mutations a protein can undergo, even to achieve a slight functional modification. David Klinghoffer summarizes their findings:
To get one protein (A) to do the job of another (B), not a completely novel protein just a slight but functional modification, Axe working together with Ann Gauger found that it would take at the very least seven or more mutations. That doesn’t sound so bad, but what would it mean in the real world of a bacterial population? Axe gives the bottom line, a distressing one for Darwinian theorists:
It turns out once you get above the number six [changes] — and even at lower numbers actually — but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
So let’s say you’re looking at a transition between two proteins that needs eight or nine steps. You’re out of luck, buddy, because six is the most that unguided evolution can do. This by itself would seem to present a devastating rebuke to any Darwinian account of how proteins, the fundamental structures of all cellular life, came to be as they are.
So much for Photosystem II. What about Photosystem I? Photosystem I is believed to have appeared earlier in the history of life on Earth than Photosystem II, since a photosystem very similar to it is present in purple and green bacteria, while Photosystem II is unique to cyanobacteria, plants and algae. So you might be thinking that Photosystem I is nice and simple, right? Wrong! This is what Photosystem I looks like in plants:
Photosystem I, as found in plants. Structure of Photosystem I created with Pymol from PDB 2o01. Courtesy of Curtis Neveu and Wikipedia.
And here’s what it looks like in cyanobacteria:
Crystal structure of Photosystem I in cyanobacteria: a photosynthetic reaction center and core antenna system. Courtesy of Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute, and Wikipedia.
According to Wikipedia, most scientists believe that Photosystem I found in plants, algae and cyanobacteria is derived from an analogous photosystem found in green-sulfur bacteria. But even if they were right, the photosystem found in green-sulfur bacteria is formidably complex, as we saw above, and we still have to account for where it comes from.
Earlier, we discussed the Z-scheme, a chain of events coupling the activity of two protein complexes, known as photosystem (PS) II and I. For those readers who have sharp eyes, here’s what it looks like (and for those who haven’t, here’s a better picture):
The Z-scheme. Courtesy of Wikipedia.
Finally, it was pointed out above that in plants, algae and cyanobacteria, the second, light-independent stage of photosynthesis produces sugars by a process known as the Calvin cycle. Here’s what it looks like:
Overview of the Calvin Cycle pathway. Courtesy of Mike Jones and Wikipedia.
Now I hope readers can see why many scientists were inclined to believe (until recently) that the dazzlingly complex process we call oxygenic photosynthesis (which occurs in plants, algae and cyanobacteria) may have taken two billion years to evolve (see for instance this paper). The work of Dr. Sean Crowe and his team strongly suggests that this complex form of photosynthesis may have appeared very early in the history of life on Earth. And as we’ve seen, even the simpler versions of photosynthesis require complexes of several kinds of proteins to work properly – proteins whose evolution cannot be accounted for by natural selection, as the pioneering work of Dr. Douglas Axe has shown. I’ll just quote one paragraph from his paper, The Case Against a Darwinian Origin of Protein Folds, in BioComplexity 2010(1):1-12. doi:10.5048/BIO-C.2010.1:
Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin. (p. 11)
As scientists digest the new findings of Dr. Crowe’s team, are they going to follow the evidence where it leads, towards Intelligent Design? Or are they going to resort to “evolution of the gaps” once more?
I’d like to conclude by recalling what Nobel Laureate physicist Robert Laughlin had to say about this kind of sloppy thinking:
Much of present-day biological knowledge is ideological. A key symptom of ideological thinking is the explanation that has no implications and cannot be tested. I call such logical dead ends antitheories because they have exactly the opposite effect of real theories: they stop thinking rather than stimulate it. Evolution by natural selection, for instance, which Charles Darwin originally conceived as a great theory, has lately come to function more as an antitheory, called upon to cover up embarrassing experimental shortcomings and legitimize findings that are at best questionable and at worst not even wrong. Your protein defies the laws of mass action? Evolution did it! Your complicated mess of chemical reactions turns into a chicken? Evolution! The human brain works on logical principles no computer can emulate? Evolution is the cause!
–Robert B. Laughlin, A Different Universe: Reinventing Physics from the Bottom Down (New York: Basic Books, 2005), pp. 168-169.
Professor Laughlin is not an Intelligent Design theorist: he subscribes to an interesting theory called Cell Intelligence. Personally, I can’t see how this theory could shed light on the origin of photosynthesis. However, Professor Laughlin is to be commended for having the courage to think “out of the box” and defy the scientific mainstream. Let’s hope that other scientists continue to break ranks from the Darwinist consensus, in the future.