A 3d cartoon depiction of the activated RuBisCO from spinach in open form with active site accessible. The active site Lys175 residues are marked in pink, and a close-up of the residue is provided to the right for one of the monomers composing the enzyme.
So, let’s look at the evolution of photosynthesis and especially the essential enzyme RuBisCo and the implications of recent research by a team from the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany in collaboration with scientists from the University of Singapore.
As regular readers will be aware from previous articles I've written, RuBisCo (full name: ribulose-1,5-bisphosphate carboxylase/oxygenase), is a major embarrassment for Creationists because it illustrates how an unintelligent design can become embedded in evolving species, despite its poor design. RuBisCo is not only the most abundant enzyme on Earth, but also almost certainly the least efficient. Indeed, its inefficiency is the reason for its abundance, in that the plants in which it is an essential enzyme, have to make up in quantity what RuBisCo lacks in quality. The total weight of RuBisCo in the world exceeds the total weight of all the humans.
RuBisCo is an essential component of photosynthesis - the process upon which almost all life on Earth ultimately depends, because it turns inorganic carbon dioxide (CO2) and water into organic glucose plus oxygen (O2) using sunlight as the energy source. This is then used by plants or by the herbivores that consume plants or the carnivores that consume the herbivores. Only a few species of single-celled organisms use some other process to obtain nutrients. It's job is to take 6 molecules of inorganic CO2 and 6 molecules of water (H2O) and, using just the energy in sunlight, make a molecule of glucose (C6H12O6) which is then used as the energy source and as the basic building block for many structural and storage carbohydrates such as cellulose, lignin (wood), starch, glycogen, etc. This forms the very basis of almost all food chains. It also, in the process, makes 6 molecules of O2 as a waste product.
RuBisCo arose on the early Earth when the atmosphere contained almost no O2. In fact atmospheric O2 is only there because of the action of RuBisCo, hence it was 'designed' in the absence of O2, and it shows!
Not only is RuBisCo painfully slow at what it does, only managing about 4 reactions per second, compared to the hundreds or thousands, even tens of thousands of reactions some enzymes manage, but it often 'mistakes' a molucules of O2 for a molecule of CO2, which stops the process in its tracks, wastes energy and creates a toxic by-product which accumulates and poisons the plant cell.
All in all, the enzyme on which almost all life on Earth depends, is so badly designed that it betrays the lack of intelligence and foresight in its design. It worked, and the single-celled organisms with it had a significant advantage over those without it, in that water, sunlight and CO2 were all readily available almost anywhere on or near the surface of the Earth. Later, when the prokaryote cyanobacteria containing it became incorporated into the eukaryote cells of plants, these also had a significant advantage over plants without it, so they came to dominate plant life on Earth, albeit each Chloroplast in each green cell in each plant endowed with a massively inefficient method for fixing inorganic carbon and building it into organic compounds, but despite its inefficiency, it is hugely preferable to not having it.
But there is even more embarrassment to come for Creationists, because recent research by scientists at the Max-Planck-Institute for Terrestrial Microbiology and from Singapore University have shown that there was an attempt to improve things early on in the evolution of RuBisCo, but that improvement only went partway towards improving efficiency by dealing with the increasing concentration of O2 in the environment. From an intelligent [sic] design advocate's point of view, the designer was aware of its blunder and tried to improve it, but gave up when it proved to be too difficult.
As the Max-Planck-Institute for Terrestrial Microbiology news release explains:
The central biocatalyst in photosynthesis, Rubisco, is the most abundant enzyme on earth. By reconstructing billion-year-old enzymes, a team of Max Planck Researchers has deciphered one of the key adaptations of early photosynthesis. Their results not only provide insights into the evolution of modern photosynthesis but also offer new impulses for improving it.In summary, instead of modifying RuBisCo to reject molecules of O2 and have greater specificity for CO2, Creationists would have us believe their intelligent [sic] designer decided instead to include a molecule that appears to modify the chance occurrences of mutations so that some small mutations have a large effect, and so increases the chances of evolving greater specificity for CO2.
Present day life fully depends on photosynthetic organisms like plants and algae that capture and convert CO2. At the heart of these processes lies an enzyme called Rubisco that captures more than 400 billion tons CO2 annually. Organisms alive today make staggering amounts of it: the mass of Rubisco on our planet outweighs that of all humans. In order to assume such a dominant role in the global carbon cycle, Rubisco had to adapt constantly to changing environmental conditions.Cryo-electron microscope image of two Rubisco complexes interacting with each other. If a subunit essential for solubility is missing, individual enzyme complexes can interact with each other in this way and form thread-like structures, so-called fibrils. Under normal conditions, however, Rubisco does not form such fibrils.© MPI f. Terrestrial Microbiology/ L. Schulz
Using a combination of computational and synthetic approaches, a team from the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany in collaboration with the University of Singapore has now successfully resurrected and studied billion-year-old enzymes in the lab. In this process, which they describe as “molecular paleontology”, the researchers found that instead of direct mutations in the active center, an entirely new component prepared photosynthesis to adapt to rising oxygen levels.
Rubisco’s early confusion
Rubisco is ancient: it emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on earth. However, with the invention of oxygen-producing photosynthesis and rise of oxygen in the atmosphere, the enzyme started catalyzing an undesired reaction, in which it mistakes O2 for CO2 and produces metabolites that are toxic to the cell. This confused substrate scope still scars Rubiscos to date and limits photosynthetic efficiency. Even though Rubiscos that evolved in oxygen-containing environments became more specific for CO2 over time, none of them could get completely rid of the oxygen capturing reaction.
The molecular determinants of increased CO2 specificity in Rubisco remain largely unknown. However, they are of great interest to researchers aiming to improve photosynthesis. Interestingly, those Rubiscos that show increased CO2 specificity recruited a novel protein component of unknown function. This component was suspected to be involved in increasing CO2 specificity, however, the true reason for its emergence remained difficult to determine because it already evolved billions of years ago.
Studying evolution by resurrecting ancient proteins in the lab
To understand this key event in the evolution of more specific Rubiscos, collaborators at the Max Planck Institute for Terrestrial Microbiology in Marburg and Nanyang Technological University in Singapore used a statistical algorithm to recreate forms of Rubiscos that existed billions of years ago, before oxygen levels began to rise. The team led by Max Planck researchers Tobias Erb and Georg Hochberg resurrected these ancient proteins in the lab to study their properties. In particular, the scientists wondered whether Rubisco’s new component had anything to do with the evolution of higher specificity.
The answer was surprising, as doctoral researcher Luca Schulz explains:
We expected the new component to somehow directly exclude oxygen from Rubisco catalytic center. That is not what happened. Instead, this new subunit seems to act as a modulator for evolution: recruitment of the subunit changed the effect that subsequent mutations had on Rubisco’s catalytic subunit. Previously inconsequential mutations suddenly had a huge effect on specificity when this new component was present. It seems that having this new subunit completely changed Rubisco’s evolutionary potential.
An enzyme’s addiction to its new subunit
This function as an “evolutionary modulator” also explains another mysterious aspect of the new protein component: Rubiscos that incorporated it are completely dependent on it, even though other forms of Rubisco can function perfectly well without. The same modulating effect explains why: When bound to this small protein component, Rubisco become tolerant to mutations that would otherwise be catastrophically detrimental. With the accumulation of such mutations, Rubisco effectively became addicted to its new subunit.Side (left) and top view of Rubisco.
© MPI for terrestrial Microbiology / L. Schulz
Altogether the findings finally explain the reason why Rubisco kept this new protein component around ever since it encountered it. Max Planck Research Group Leader Georg Hochberg explains:
The fact that this connection was not understood until now highlights the importance of evolutionary analysis for understanding the biochemistry that drives life around us. The history of biomolecules like Rubisco can teach us so much about why they are the way they are today. And there are still so many biochemical phenomena whose evolutionary history we really have no idea about. So it’s a very exciting time to be an evolutionary biochemist: almost the entire molecular history of the cell is still waiting to be discovered.
It's almost as though this supposedly intelligent [sic] designer believes in evolution and so knew that, because of the randomness of mutation, the actual direction of evolution was unpredictable, so it tweaked the design in some species of plant to increase the chances of a beneficial mutation. The descendants of plants with those tweaks continue to carry it, even though the evolutionary process didn't produce what the designer hoped for. So much for omniscience!
To a biologist of course, the inclusion of a molecule which improved the evolvability of RuBisCo will be unsurprising since there are many examples in nature of evolvability itself evolving because evolvability is advantageous in a changing environment and often makes the difference between success and extinction.
And still RuBisCo carries on in its ponderous way, wasting resources because it is so badly designed. And still creationist frauds fool their dupes into believing that it was the work of an intelligent, omniscient god using god-magic. It's easier for people with the thinking ability of toddlers, the superstitions of Bronze Age pastoralists and the need to feel super special, to believe that, than to try to understand how evolution works.
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