Unintelligent Design News - If Scientists Can Do It, Why Couldn't Creationism's 'Intelligent' Designer?

© Max Planck Institute for Terrestrial Microbiology/Geisel

First step towards synthetic CO₂ fixation in living cells | Max Planck Institute for Terrestrial Microbiology

I've written several articles on one of the best arguments against intelligent design - RuBisCo - and include a section on it in The Unintelligent Designer: Refuting The Intelligent Design Hoax. I have also reported on efforts by biomedical scientists to improve on its efficiency and so increase crop yields.

Now we have another research paper which shows how any intelligent designer of photosynthesis could have done a much better job of it but either chose not to or was too incompetent to realise is could have done better, if it really is intelligently [sic] designed and not the result of a mindless, utilitarian process.

First a little refresher on RuBisCo and why it is so inefficient:

Tell me all about RuBisCo (ribulose-1,5-bisphosphate carboxylase/oxygenase), what it does, how it evolved and why it is so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is a crucial enzyme involved in photosynthesis, the process by which plants, algae, and some bacteria convert carbon dioxide (CO₂) into organic compounds using the energy from sunlight. It plays a central role in the Calvin cycle, which is the second stage of photosynthesis.

Function:

1. Carboxylation: RuBisCo catalyzes the carboxylation of ribulose-1,5-bisphosphate (RuBP) by adding a carbon dioxide molecule (CO₂). This results in the formation of two molecules of 3-phosphoglycerate (3-PGA), which are then converted into sugars and other organic molecules in subsequent metabolic pathways. Reaction: CO₂ + RuBP → 2 molecules of 3-PGA
2. Oxygenation: In addition to its carboxylase activity, RuBisCo also has oxygenase activity. It can react with oxygen instead of carbon dioxide, leading to the production of one molecule of 3-PGA and one molecule of 2-phosphoglycolate. The latter needs to be processed in a series of reactions called photorespiration, which consumes energy and reduces the overall efficiency of photosynthesis.
   
   Reaction: O2 + RuBP → 3-PGA + 2-phosphoglycolate

Evolution:

RuBisCo is believed to be one of the oldest enzymes, dating back to the early stages of Earth's atmosphere when oxygen levels were low. Its inefficiency in discriminating between CO₂ and O2 likely stems from the fact that it evolved in an environment where oxygen was scarce. As atmospheric oxygen levels increased, the oxygenase activity became a significant drawback, leading to the evolution of various mechanisms to minimize the impact of photorespiration.

Inefficiency:

RuBisCo is often regarded as inefficient for several reasons:

1. Substrate specificity: RuBisCo has a low affinity for carbon dioxide, and it competes with oxygen for binding to the active site. This dual specificity results in a wasteful process (photorespiration) that diminishes the overall efficiency of carbon fixation.
2. Slow catalysis: RuBisCo is a relatively slow enzyme, limiting the rate at which carbon dioxide is fixed during photosynthesis.
3. Large size: RuBisCo is a large and complex protein, requiring substantial resources for synthesis and maintenance within plant cells.

Efforts are underway to engineer more efficient forms of RuBisCo and to explore alternative pathways for carbon fixation to improve the overall efficiency of photosynthesis. Improving RuBisCo's performance is a key focus in plant biotechnology and genetic engineering to enhance crop productivity and address global food security challenges.

The discovery that RuBisCo could have been more efficiently designed is the result of experiments to increase the rate of CO₂ capture to reduce global warming and climate change because the second stage of photosynthesis is 'carbon capture', and the inefficiency of RuBisCo in doing this is the rate-limiting factor in photosynthesis.

There are two enzymes, each of which is found in bacteria, so creationists will have difficulty explaining why an intelligent designer didn't use them in its design of RuBisCo. These are crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase, each of which is capable of fixing CO₂ more than 10 times faster than RuBisCo does.

The research by a team of scientists from the Max Planck Institute for Terrestrial Biology, is explained in a press release from the Max Planck Institute:

Synthetic biology offers the opportunity to build biochemical pathways for the capture and conversion of carbon dioxide (CO₂). Researchers at the Max-Planck-Institute for Terrestrial Microbiology have developed a synthetic biochemical cycle that directly converts CO₂ into the central building block Acetyl-CoA. The researchers were able to implement each of the three cycle modules in the bacterium E.coli, which represents a major step towards realizing synthetic CO₂ fixing pathways within the context of living cells.

Developing new ways for the capture and conversion of CO₂ is key to tackle the climate emergency. Synthetic biology opens avenues for designing new-to-nature CO₂-fixation pathways that capture CO₂ more efficiently than those developed by nature. However, realizing those new-to-nature pathways in different in vitro and in vivo systems is still a fundamental challenge. Now, researchers in Tobias Erb's group have designed and constructed a new synthetic CO₂-fixation pathway, the so-called THETA cycle. It contains several central metabolites as intermediates, and with the central building block, acetyl-CoA, as its output. This characteristic makes it possible to be divided into modules and integrated into the central metabolism of E. coli.

The entire THETA cycle involves 17 biocatalysts, and was designed around the two fastest CO₂-fixing enzymes known to date: crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase. The researchers found these powerful biocatalysts in bacteria. Although each of the carboxylases can capture CO₂ more than 10 times faster than RuBisCo, the CO₂-fixing enzyme in chloroplasts, evolution itself has not brought these capable enzymes together in natural photosynthesis.

The THETA cycle converts two CO₂ molecules into one acetyl-CoA in one cycle. Acetyl-CoA is a central metabolite in almost all cellular metabolism and serves as the building block for a wide array of vital biomolecules, including biofuels, biomaterials, and pharmaceuticals, making it a compound of great interest in biotechnological applications. Upon constructing the cycle in test tubes, the researchers could confirm its functionality. Then the training began: through rational and machine learning-guided optimization over several rounds of experiments, the team was able to improve the acetyl-CoA yield by a factor of 100. In order to test its in vivo feasibility, incorporation into the living cell should be carried out step by step. To this end, the researchers divided the THETA cycle into three modules, each of which was successfully implemented into the bacterium E. coli. The functionality of these modules was verified through growth-coupled selection and/or isotopic labelling.

"What is special about this cycle is that it contains several intermediates that serve as central metabolites in the bacterium's metabolism. This overlap offers the opportunity to develop a modular approach for its implementation.” explains Shanshan Luo, lead author of the study. “We were able to demonstrate the functionality of the three individual modules in E. coli. However, we have not yet succeeded in closing the entire cycle so that E. coli can grow completely with CO₂," she adds. Closing the THETA cycle is still a major challenge, as all of the 17 reactions need to be synchronized with the natural metabolism of E. coli, which naturally involves hundreds to thousands of reactions. However, demonstrating the whole cycle in vivo is not the only goal, the researcher emphasizes. "Our cycle has the potential to become a versatile platform for producing valuable compounds directly from CO₂ through extending its output molecule, acetyl-CoA." says Shanshan Luo.

“Bringing parts of the THETA cycle into living cells is an important proof-of-principle for synthetic biology”, adds Tobias Erb. “Such modular implementation of this cycle in E. coli paves the way to the realization of highly complex, orthogonal new-to-nature CO₂-fixation pathways in cell factories. We are learning to completely reprogram the cellular metabolism to create a synthetic autotrophic operating system for the cell."

More technical detail is given in the team's open access paper in the journal Nature Catalysis:

Abstract

Synthetic biology offers the opportunity to build solutions for improved capture and conversion of carbon dioxide (CO₂) that outcompete those evolved by nature. Here we demonstrate the design and construction of a new-to-nature CO₂-fixation pathway, the reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle. The THETA cycle encompasses 17 enzymes from 9 organisms and revolves around two of the most efficient CO₂-fixing enzymes described in nature, crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase. Here using rational and machine learning-guided optimization approaches, we improved the yield of the cycle by two orders of magnitude and demonstrated the formation of different biochemical building blocks directly from CO₂. Furthermore, we separated the THETA cycle into three modules that we successfully implemented in vivo by exploiting the natural plasticity of Escherichia coli metabolism. Growth-based selection and/or ¹³C-labelling confirmed the activity of three different modules, demonstrating the first step towards realizing highly orthogonal and complex CO₂-fixation pathways in the background of living cells.

Main

Biological carbon fixation assimilates more than 380 gigatons of carbon dioxide (CO₂) annually and plays an essential role in the global carbon cycle as a major carbon sink¹. This makes biological carbon fixation key for any efforts of re-balancing the global carbon cycle and mitigating the effects of climate change². In nature, plants, algae and other autotrophs convert CO₂ into organic molecules through CO₂-fixation pathways. So far, seven natural CO₂-fixation pathways have been discovered^3,4. All of them have different physiological properties and are adapted to certain environmental conditions⁵. Despite this biological diversity, nature has only occupied a very limited solution space, indicating that many theoretically possible CO₂-fixation pathways have not been explored or were selected for by evolution⁶.

With the emergence of synthetic biology, it has become possible to realize these new-to-nature solutions from the first principles by combining freely the entire repertoire of enzymes, reactions and mechanisms⁷. So far, more than 30 new-to-nature CO₂-fixation pathways have been designed theoretically^6,8,9. Two oxygen-insensitive designs, the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle and the reductive glyoxylate and pyruvate synthesis-malyl-CoA-glycerate (rGPS-MCG) cycle, have been realized in vitro^10,11, offering different possibilities for sustainable biosynthesis and cell-free biology^12,13.

Yet, an open challenge is the feasibility of new-to-nature pathways in vivo. Importantly, this challenge scales with the complexity and orthogonality of the pathway design, as the potential to create more unwanted interactions with the native genetic and metabolic network of a cell increases with increasing size of the metabolic network¹⁴. While naturally existing CO₂-fixation pathways have been successfully transferred to Escherichia coli and other model organisms through the expression of a handful genes^15,16,17,18, the proof of principle is still outstanding for new-to-nature CO₂-fixation pathways that feature several orthogonal metabolites and reactions that do not share any overlap with the central carbon metabolism of the host. The implementation of new-to-nature CO₂-fixation pathways in vivo, however, is a necessary step, not only to broaden their applications and impact, but also to examine their real-life performance and compare them with their natural counterparts to gain more insights into the evolution and limitation of carbon fixation in the context of living cells.

In this Article, we show the successful design, realization and optimization of a synthetic CO₂-fixation pathway, the reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle, by using rational design and machine learning. The THETA cycle converts CO₂ directly into the central building block acetyl-CoA, which makes it potentially a versatile platform for the synthesis of value-added compounds from CO₂ (ref. ¹²). Notably, we also demonstrate how the THETA cycle can be modularized and transferred to E. coli, which paves the way for the complete implementation and adaptive evolution of this new-to-nature CO₂-fixation cycle in the future.

Fig. 1: The THETA cycle and its realization.

a, The overall strategy used in this work to establish the THETA cycle. The THETA cycle was designed in three modules, constructed in vitro, optimized through rational approaches and machine learning, before its three modules were implemented in E. coli. b, The scheme of the THETA cycle. Inner circle: simplified scheme of the THETA cycle, consisting of three pathway modules. Outer circle: detailed scheme of the THETA cycle. The conditions for Δ_rG′^m are at 25 °C, 1 bar pressure, pH 7.0, pMg 3, ionic strength 0.25 M and 1 mM for all reactants. The calculation details of Δ_rG′^m can be found at ref. ¹². For enzyme abbreviations, see Supplementary Table 2. ML, machine learning.

As though RuBisCo with all its inefficiency and bad design, wasn't bad enough for the creationist industry, we now have evidence that it could have been over ten times faster it if really had been intelligently designed by an omniscient designer who had already designed two enzymes that did the job more efficiently. It's hard to see how creationists can blame this on 'Satan' or 'Sin' since their favourite chapter of the Bible describes how their putative designer designed plants, albeit before there was a sun to provide photons for their photosynthetic process.

But perhaps the real problem for creationists is in explaining how scientists using science can do something their supposedly omnipotent god couldn't do.

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