Despite ludicrous claims by Creationist frauds and their dupes that the Theory of Evolution (TOE) is about to be abandoned by mainstream biomedical science and replaced by an evidence-free Bronze Age superstition involving magic, the TOE continues to be the fundamental principle of biology and the framework which explains what can be observed, without the need for magic and unknowable mysteries.
Take for example the question of the origin of nitrogen fixation.
Nitrogen is essential for all biological organisms, being an integral part of all proteins, yet, despite the abundance of molecular nitrogen (N2) in the atmosphere at about 78%, no eukaryote organisms can extract it directly. The problem is that N2 is a very stable molecule with a triple bond between the two atoms, so, to be biologically active, it needs to be converted to ammonia (NH3) which takes an enormous amount of energy and sixteen molecules of ATP. A significant proportion of ammonia comes from lightning strikes which convert a molecule of N2 and three molecules of water (H2O) into two molecules of NH3 and a molecule of ozone (O3)
N2 + 3H2O → 2NH3 + O3
But by far the most significant source of biological nitrogen is 'nitrogen fixation' by bacteria living often in symbiosis with plants. One example is nitrogen fixation by prokaryote bacteria is the relationship between rhizobia bacteria (Rhizobiaceae, α-Proteobacteria) which live in nodules in the roots of plants of the legume family. Other free-living nitrogen-fixing bacteria contribute to soil and marine nitrogen when the nitrogen in their bodies is released when they die.
Nitrogen Fixation by Legumes (Guide A-129) - New Mexico State University
The question for evolutionary biology was where and when did this ability to fix nitrogen originate? The prevailing consensus was that it originated in archaea and was acquired by bacteria by horizontal gene transfer. That consensus has now been challenged by a team of researchers from National Chung Hsing University and Academia Sinica, Taiwan, in an open access paper which argues that the process arose in bacteria first and was acquired by archaea later.The evidence is in the form of an in-depth analysis of the >30,000 prokaryotic genomes that have so far been sequenced, to test the two competing hypotheses. This analysis produced nested hierarchies, in which the nitrogen-fixing archaea were nested inside the bacterial clades, and the fact that the majority of archaea use the bacterial Mo (molybdenum) transporter (ModABC) and not the archaeal Mo transporter (WtpABC). In other words, the majority of archaea use the bacterial process, not the archaeal process.
These observations, of course, only make any sense as the result of an evolutionary process. Certainly, there is no evidence of intelligent design here. After all, why design two different methods to achieve the same result. Also, why not designs eukaryotes to fix nitrogen directly by giving them the same processes used in bacteria and archaea, or one less demanding of energy, instead of opting for the much more complex system of symbiosis and dependence on dead bacteria releasing their fixed nitrogen?
In evolutionary terms of course, there was no evolutionary pressure on eukaryotes to evolve independent nitrogen fixation because bacteria and archaea were already abundant when the first eukaryotes and the first multicellular organisms arose, so biological nitrogen was not in short supply. That situation did not apply in the early evolution of the prokaryotes, for whom nitrogen would have been in very short supply, so the expenditure of energy in the process of fixing atmospheric nitrogen was cost-effective.
The resulting eukaryote plant life evolved to fit the environment in which they were evolving. The additional energy needed by an independent nitrogen fixing metabolic process would have made any evolution in that direction, deleterious, so it never evolved. For the legumes, it proved advantageous with little additional resource, to have nitrogen fixing bacteria living symbiotically in their roots.
An example there of how the process of evolution by natural selection results in a compromise solution which tends to provide the greatest benefit for the least cost.
Copyright: © 2022 The authors.Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access. (CC BY-NC 4.0)
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
Hong-Wei Pi, Jinn-Jy Lin, Chi-An Chen, Po-Hsiang Wang, Yin-Ru Chiang, Chieh-Chen Huang, Chiu-Chung Young, Wen-Hsiung Li,
Origin and Evolution of Nitrogen Fixation in Prokaryotes, Molecular Biology and Evolution, 39(9), September 2022, msac181, DOI: 10.1093/molbev/msac181
Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access
Reprinted under a Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
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