Nitrogen fixation, Photosynthesis, and Energy cycles: The amazing interdependence that points to design
https://reasonandscience.catsboard.com/t2680-nitrogen-fixation-photosynthesis-and-energy-cycles-the-amazing-interdependence-that-points-to-design
Cyanobacteria are the most numerous and probably most important and fundamental organisms on the planet. There are more of them on Earth than there are observable stars in the Universe and these little creatures are what enabled you – and every other complex living thing that has ever lived on the planet, from dinosaurs to daffodils – to exist.
Ammonia through Nitrogen fixation
Nitrogen is an essential component of amino acids. Earth has an abundant supply of nitrogen, but it is primarily in the form of atmospheric nitrogen gas (N2), a remarkably inert molecule. Thus, a fundamental problem for biological systems is to obtain nitrogen in a more usable form. This problem is solved by cyanobacteria ( amongst a few other bacterias and archaea ) capable of reducing the inert N = N triple-bond molecule of nitrogen gas to two molecules of ammonia in one of the most amazing reactions in biochemistry through Nitrogenase enzymes : Nitrogen in the form of ammonia is the source of nitrogen for all the amino acids. The carbon backbones come from the glycolytic pathway, the pentose phosphate pathway, or the citric acid cycle in cellular metabolism.
Oxygen is produced
through photosynthesis. Without Oxygen, there would be no advanced life on earth possible.
Glucose
Glucose is a ubiquitous fuel in biology. It is used as an energy source in most organisms, from bacteria to humans, through either aerobic respiration, anaerobic respiration, or fermentation. Glucose is the human body's key source of energy. Through glycolysis and later in the reactions of the citric acid cycle and oxidative phosphorylation, glucose is oxidized to eventually form CO2 and water, yielding energy mostly in the form of ATP.
Nitrogenase:
Is a monstrously complicated enzyme, and central to life on our planet.
Oxygenic photosynthesis is itself the most complex metabolic machine known in nature requiring 26 protein complexes and enzymes.
Now think about this: Nitrogenase and Oxygenic Photosynthesis are INTERDEPENDENT.
That is: The Nitrogenase enzyme is powered by ATP ( the energy currency of the cell ) ; it requires. both - the electrons and the ATP in this system are provided through photosynthesis. Inherently, photosynthesis generates oxygen gas, while concurrently generating protons and electrons. The electrons pass through a series of electron carriers to finally reduce ferredoxin or flavodoxin. These are iron-sulfur proteins that mediate electron transfer in a range of metabolic reactions - in our case, they handle electrons to NItrogenase.
In the nitrogenase reaction, electrons from reduced ferredoxin pass to nitrogenase reductase, which serves as an electron donor to nitrogenase, the enzyme that actually catalyzes N2 fixation. Electron transfer from nitrogenase reductase to nitrogenase takes place through docking of nitrogenase reductase with an ab-subunit pair of nitrogenase. Nitrogenase catalyzes an OPTIMAL reaction. Nitrogenase is composed of two component proteins, one called the Fe protein (also called component II or dinitrogenase reductase) and the other called the MoFe protein (also called component I or dinitrogenase), which work together as a molecular machine to catalyze the reduction of N2 ammonia.
The Fe protein functions as a reductant of the MoFe protein, transferring one electron at a time from its [4Fe–4S] cluster to the MoFe protein in a reaction linked to the hydrolysis of MgATP. As part of the dynamics of the process, the Fe protein dissociates from its partner MoFe protein following each electron transfer event, allowing the Fe protein to be recharged by reduction and replacement of the spent nucleotides with MgATP. A minimum of eight such association/ dissociation events is required for each N2 reduced.
My comment: None of the eight intermediate stages meets the goal to split nitrogen. Let me outline this. The author of above paper mentions an " optimal reaction", which is achieved by two components working together as a molecular machine !! That raises the question: Why would natural selection or any evolutionary mechanism evolve such intermediate stages if there is no survival advantage to be gained by it ? This is an all or nothing business. Either the whole process goes through eight times, or nitrogen is not split.
Now consider other amazing facts: Photosynthesis produces oxygen. But oxygen is poisonous for Nitrogenase. So there must be mechanisms to protect oxygen-sensitive nitrogenase from photosynthetic oxygen. There are several such mechanisms, but the most remarkable one is the separation of Nitrogen-fixing in cells called heterocysts, and photosynthesis happens in other cells, called vegetative cells. As such, Cyanobacteria can be multicellular organisms, and divide tasks by promoting an ultracomplex process of cellular differentiation.
And: The formation of multicellular organisms from the assembly of single-celled ones constitutes one of the most striking and complex problems tackled by biology. Multicellularity involves at least three welldefined processes: cell-cell adhesion, intercellular communication, and cell differentiation. These had to emerge together since if one is missing, nothing done.
I will not go into other issues, like how all these molecular machines are assembled, which is another issue, but I will finish with this: Consider that almost all these proteins require complex metal clusters, which all must be just right, and imported by complex mechanisms from the outside of the cell, then some materials must be transformed, like Iron, into useful form, the cofactor metal clusters must be assembled, and then correctly inserted into the proteins, and then, the proteins must be brought to the assembly place, and correctly assembled into functional machine complexes.
Another thing. All this requires fully functional, interdependent Energy cycles.
BIOGEOCHEMICAL CYCLING OF MINERAL-FORMING ELEMENTS, page 25
"The five element cycles are clearly interdependent and any change in one cycle will in the long term have a profound influence on the operation of the other four."
How could all this have emerged in a slow, stepwise, evolutionary process? Shall we have a look, what secular science papers say?
New insights into the evolutionary history of biological nitrogen fixation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733012/
Since extant nitrogenase functions to relieve N limitation in ecosystems, the imbalance in the supply and demand for fixed N is thought to have represented a strong selective pressure that may have precipitated the emergence of nitrogen fixation.
So - pure guesswork.
Photosynthesis?
“The process of photosynthesis is a very complex set of interdependent metabolic pathways “How it could have evolved is a bit mysterious.”
Robert Blankenship, professor of biochemistry at Arizona State University
More:
The Nitrogenase enzyme, the molecular sledgehammer
https://reasonandscience.catsboard.com/t1585-nitrogenase#2406
Cyanobacterias, amazing evidence of design
https://reasonandscience.catsboard.com/t1551-cyanobacteria-amazing-evidence-of-design
Main topics on photosynthesis
https://reasonandscience.catsboard.com/t2653-maintopics-on-photosynthesis
The nitrogenase complex is composed of two metalloproteins
https://reasonandscience.catsboard.com/t2590-molecular-biochemistry-biology-the-origin-of-life-and-biodiversity-sistematically-analyzed-from-a-universal-perspective#5867
Energy cycles, how did they "take off" ?
https://reasonandscience.catsboard.com/t2660-energy-cycles-how-did-they-took-off
Biosynthesis of Iron-sulfur clusters, basic building blocks for life
https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life
Iron Uptake and Homeostasis in Cells
https://reasonandscience.catsboard.com/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms
Glucose and its importance for life
https://reasonandscience.catsboard.com/t2158-glucose-and-its-importance-for-life
Availability of ammonia in a prebiotic earth
https://reasonandscience.catsboard.com/t2689-availability-of-ammonia-in-a-prebiotic-earth
https://reasonandscience.catsboard.com/t2680-nitrogen-fixation-photosynthesis-and-energy-cycles-the-amazing-interdependence-that-points-to-design
Cyanobacteria are the most numerous and probably most important and fundamental organisms on the planet. There are more of them on Earth than there are observable stars in the Universe and these little creatures are what enabled you – and every other complex living thing that has ever lived on the planet, from dinosaurs to daffodils – to exist.
Ammonia through Nitrogen fixation
Nitrogen is an essential component of amino acids. Earth has an abundant supply of nitrogen, but it is primarily in the form of atmospheric nitrogen gas (N2), a remarkably inert molecule. Thus, a fundamental problem for biological systems is to obtain nitrogen in a more usable form. This problem is solved by cyanobacteria ( amongst a few other bacterias and archaea ) capable of reducing the inert N = N triple-bond molecule of nitrogen gas to two molecules of ammonia in one of the most amazing reactions in biochemistry through Nitrogenase enzymes : Nitrogen in the form of ammonia is the source of nitrogen for all the amino acids. The carbon backbones come from the glycolytic pathway, the pentose phosphate pathway, or the citric acid cycle in cellular metabolism.
Oxygen is produced
through photosynthesis. Without Oxygen, there would be no advanced life on earth possible.
Glucose
Glucose is a ubiquitous fuel in biology. It is used as an energy source in most organisms, from bacteria to humans, through either aerobic respiration, anaerobic respiration, or fermentation. Glucose is the human body's key source of energy. Through glycolysis and later in the reactions of the citric acid cycle and oxidative phosphorylation, glucose is oxidized to eventually form CO2 and water, yielding energy mostly in the form of ATP.
Nitrogenase:
Is a monstrously complicated enzyme, and central to life on our planet.
Oxygenic photosynthesis is itself the most complex metabolic machine known in nature requiring 26 protein complexes and enzymes.
Now think about this: Nitrogenase and Oxygenic Photosynthesis are INTERDEPENDENT.
That is: The Nitrogenase enzyme is powered by ATP ( the energy currency of the cell ) ; it requires. both - the electrons and the ATP in this system are provided through photosynthesis. Inherently, photosynthesis generates oxygen gas, while concurrently generating protons and electrons. The electrons pass through a series of electron carriers to finally reduce ferredoxin or flavodoxin. These are iron-sulfur proteins that mediate electron transfer in a range of metabolic reactions - in our case, they handle electrons to NItrogenase.
In the nitrogenase reaction, electrons from reduced ferredoxin pass to nitrogenase reductase, which serves as an electron donor to nitrogenase, the enzyme that actually catalyzes N2 fixation. Electron transfer from nitrogenase reductase to nitrogenase takes place through docking of nitrogenase reductase with an ab-subunit pair of nitrogenase. Nitrogenase catalyzes an OPTIMAL reaction. Nitrogenase is composed of two component proteins, one called the Fe protein (also called component II or dinitrogenase reductase) and the other called the MoFe protein (also called component I or dinitrogenase), which work together as a molecular machine to catalyze the reduction of N2 ammonia.
The Fe protein functions as a reductant of the MoFe protein, transferring one electron at a time from its [4Fe–4S] cluster to the MoFe protein in a reaction linked to the hydrolysis of MgATP. As part of the dynamics of the process, the Fe protein dissociates from its partner MoFe protein following each electron transfer event, allowing the Fe protein to be recharged by reduction and replacement of the spent nucleotides with MgATP. A minimum of eight such association/ dissociation events is required for each N2 reduced.
My comment: None of the eight intermediate stages meets the goal to split nitrogen. Let me outline this. The author of above paper mentions an " optimal reaction", which is achieved by two components working together as a molecular machine !! That raises the question: Why would natural selection or any evolutionary mechanism evolve such intermediate stages if there is no survival advantage to be gained by it ? This is an all or nothing business. Either the whole process goes through eight times, or nitrogen is not split.
Now consider other amazing facts: Photosynthesis produces oxygen. But oxygen is poisonous for Nitrogenase. So there must be mechanisms to protect oxygen-sensitive nitrogenase from photosynthetic oxygen. There are several such mechanisms, but the most remarkable one is the separation of Nitrogen-fixing in cells called heterocysts, and photosynthesis happens in other cells, called vegetative cells. As such, Cyanobacteria can be multicellular organisms, and divide tasks by promoting an ultracomplex process of cellular differentiation.
And: The formation of multicellular organisms from the assembly of single-celled ones constitutes one of the most striking and complex problems tackled by biology. Multicellularity involves at least three welldefined processes: cell-cell adhesion, intercellular communication, and cell differentiation. These had to emerge together since if one is missing, nothing done.
I will not go into other issues, like how all these molecular machines are assembled, which is another issue, but I will finish with this: Consider that almost all these proteins require complex metal clusters, which all must be just right, and imported by complex mechanisms from the outside of the cell, then some materials must be transformed, like Iron, into useful form, the cofactor metal clusters must be assembled, and then correctly inserted into the proteins, and then, the proteins must be brought to the assembly place, and correctly assembled into functional machine complexes.
Another thing. All this requires fully functional, interdependent Energy cycles.
BIOGEOCHEMICAL CYCLING OF MINERAL-FORMING ELEMENTS, page 25
"The five element cycles are clearly interdependent and any change in one cycle will in the long term have a profound influence on the operation of the other four."
How could all this have emerged in a slow, stepwise, evolutionary process? Shall we have a look, what secular science papers say?
New insights into the evolutionary history of biological nitrogen fixation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733012/
Since extant nitrogenase functions to relieve N limitation in ecosystems, the imbalance in the supply and demand for fixed N is thought to have represented a strong selective pressure that may have precipitated the emergence of nitrogen fixation.
So - pure guesswork.
Photosynthesis?
“The process of photosynthesis is a very complex set of interdependent metabolic pathways “How it could have evolved is a bit mysterious.”
Robert Blankenship, professor of biochemistry at Arizona State University
More:
The Nitrogenase enzyme, the molecular sledgehammer
https://reasonandscience.catsboard.com/t1585-nitrogenase#2406
Cyanobacterias, amazing evidence of design
https://reasonandscience.catsboard.com/t1551-cyanobacteria-amazing-evidence-of-design
Main topics on photosynthesis
https://reasonandscience.catsboard.com/t2653-maintopics-on-photosynthesis
The nitrogenase complex is composed of two metalloproteins
https://reasonandscience.catsboard.com/t2590-molecular-biochemistry-biology-the-origin-of-life-and-biodiversity-sistematically-analyzed-from-a-universal-perspective#5867
Energy cycles, how did they "take off" ?
https://reasonandscience.catsboard.com/t2660-energy-cycles-how-did-they-took-off
Biosynthesis of Iron-sulfur clusters, basic building blocks for life
https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life
Iron Uptake and Homeostasis in Cells
https://reasonandscience.catsboard.com/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms
Glucose and its importance for life
https://reasonandscience.catsboard.com/t2158-glucose-and-its-importance-for-life
Availability of ammonia in a prebiotic earth
https://reasonandscience.catsboard.com/t2689-availability-of-ammonia-in-a-prebiotic-earth
