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Availability of ammonia in a prebiotic earth

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1 Availability of ammonia in a prebiotic earth on Thu Feb 22, 2018 5:21 am

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Availability of ammonia in a prebiotic earth

http://reasonandscience.catsboard.com/t2689-availability-of-ammonia-in-a-prebiotic-earth



Ammonia is an essential building block for amino acids, which are the building blocks of proteins.  All amino acids are derived from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen enters these pathways by way of glutamate and glutamine. 3 The major pathway by which ammonia is incorporated into amino acids is through the reductive amination of α‐ketoglutarate to glutamate. Ammonia is highly toxic for animals. Glutamine is a nontoxic carrier of ammonia. 2 

THEORIES for the origin of life require the availability of reduced (or 'fixed') nitrogen-containing compounds, in particular ammonia. In reducing atmospheres, such compounds are readily formed by electrical discharges but geochemical evidence suggests that the early Earth had a non-reducing atmosphere in which discharges would have instead produced NO ( Nitrogen oxide may refer to a binary compound of oxygen and nitrogen, or a mixture of such compounds ). This would have been converted into nitric and nitrous acids and delivered to the early oceans as acid rain. It is known, however, that Fe(II) was present in the early oceans at much higher concentrations than are found today, and thus the oxidation of Fe(II) to Fe(III) provides a possible means for reducing nitrites and nitrates to ammonia. Here we explore this possibility in a series of experiments which mimic a broad range of prebiotic seawater conditions (the actual conditions on the early Earth remain poorly constrained). We find that the reduction by Fe(II) of nitrites and nitrates to ammonia could have been a significant source of reduced nitrogen on the early Earth, provided that the ocean pH exceeded 7.3 and is favoured for temperatures greater than about 25 °C. 6

The current view is that nitrogen was most likely released into the atmosphere as dinitrogen. 7 .According to current hypotheses, terrestrial atmospheres are formed from the release of gases originally trapped in the solid interior of the planets during their final stages of accretion. The composition of these gases depends on the redox state of the mantle/crust they are released from. Geochemical and geological evidence suggests that iron migrated to the core very early in Earth’s history and volatiles outgassed from a relatively oxidized mantle, much like that of the modern Earth. Dinitrogen is one of the least reactive compounds found in nature. This is because of the very high strength of its triple, N≡N, bond. This gives it a very high dissociation energy (at 3,000°C, at standard pressure, there is no significant dissociation) and makes chemical interactions with its p system (electrons involved in the triple bond) very weak. This allows it to remain as an atmospheric component after other species have been removed. For example, nitrogen is not removed from the atmosphere by weathering, like CO2 . For this reason, the first step in atmospheric chemistry to fix nitrogen involves processes such as lightning and meteors. These produce very high temperatures, >10,000 K.  The products of such heating depend on the composition of the atmosphere being shocked. This has been modeled both theoretically and experimentally. In neutral atmospheres (i.e., atmospheres with only a few percent hydrogen or CO or less processes such as lightning, meteors, and/or coronal discharges cause the formation of nitrogen oxide (NO) and carbon monoxide (CO) . They did find hydrogen cyanide (HCN), ammonia, and amino acid production in small quantities by spark discharge in a neutral atmosphere. In a mildly reducing atmosphere (Hydrogen > ~10% and/or CO > ~5%), one observes the production of significant amounts of HCN.  HCN is a form of reduced nitrogen that can enter directly into prebiotic chemistry.  A reducing atmosphere (large amounts of CH 4 , NH 3 , and H2 or CO as major constituents) produces complex organic species that can directly lead to such compounds as amino acids though, as mentioned above, recent results make such a composition unlikely. It has been proposed that the early terrestrial planets were able to evolve significant compositions of H 2 and CO, though questions remain and amounts are uncertain.

The atmosphere is not considered to have been reducing enough for shock heating to produce amino acids as easily or abundantly as with Miller-Urey-type experiments. So how do we get to amino acids from ammonia and/or hydrogen cyanide? The most accepted route is the Strecker synthesis where ammonia, hydrogen cyanide, and an aldehyde or ketone react to form amino acids. This reaction is a likely candidate for how the amino acids in the meteorites were formed in the first place.

Nitrogen, like carbon, is essential for the formation of life. However, in many ways the sources of prebiotic nitrogen are more of an open question than sources of prebiotic carbon. The difficulty in abiotically fixing nitrogen is one reason why the removal of nitrogen from the Earth’s atmosphere is currently so heavily dominated by biology (and by a surprisingly few types of microorganisms). All of the proposed routes for the formation of prebiotic nitrogen compounds fi nd some way of overcoming the chemical inertness of N 2 (or, in the case of exogenous delivery, a way of avoiding passing through N 2 entirely). While some preliminary estimates of the magnitude of some of these sources exist, much more work needs to be done to understand what processes could have provided prebiotic nitrogen and in what forms and amounts it could have been available.

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The importance of ammonia (NH3) to the primitive atmosphere, if indeed it was present, is that its photolysis products could be precursors to prebiotic synthesis (Miller and Urey, 1959) and, in addition, by absorption of longwave radiation NH3 could produce a substantial "greenhouse effect" and maintain a surface temperature above freezing when the solar output was less than today (Sagan and Mullen, 1972). 9  if could be supposed that there was a continuous source of ammonia NH3 to the atmosphere, presumably by outgassing. Abelson (1966) first suggested that the lifetime of ammonia NH3 would be short because of its photochemical dissociation. We find that if the initial NH3 mixing ratio was 10-4 then in only 40 years the NH3 would have been destroyed through photolysis. If the mixing ratio were 10-5, then the lifetime was less than 10 years. Thus the NH3 greenhouse effect would have been restricted to the time over which outgassing occurred.

Another paper reports:  it has been argued that photodestruction of ammonia would have been substantially complete in less than <1Myr ( myr, "million years" ).  It has been claimed that any ammonia present would have been photolyzed in 30000 years or less by UV light. (  Photolysis, the chemical process by which molecules are broken down into smaller units through the absorption of light. )

8



Amino acids were among the first biological compounds found in prebiotic organic synthesis experiments (Miller 1953), and since then, a variety of mechanisms have been found by which they can be produced abiotically. 9 Depending on the starting conditions, ~12 of the 20 coded biological amino acids now have convincing prebiotic syntheses (Miller 1998). Other pathways also yield amino acids, for example, the hydrolysis of the polymer derived from the condensation of aqueous HCN (   Hydrogen cyanide ) gives rise to a variety of amino acids including serine, aspartic and glutamic acids, and α- and β-alanine (Ferris et al. 1978).

Orgel however refutes this claim by affirming that:  

The possibility that reactions of hydrogen cyanide (HCN) might form the basis for a complex cyclic organization has been proposed, but there is as yet no experimental evidence to support this proposal. 5

The hydrolysis of various high-molecular-weight organic polymers (tholins) has also been found to liberate amino acids directly (Khare et al. 1986), suggesting that solution-phase conditions may be less important than previously thought if sufficiently reducing atmospheric conditions are available. There is strong evidence for some of the aromatic amino acids (phenylalanine and tyrosine) in carbonaceous chondrites (Pizzarello and Holmes 2009); however, several biological amino acids such as histidine, tryptophan, arginine, and lysine remain difficult targets of prebiotic synthesis (Miller 1998). 4

It is unknown when proteins or simple peptides became integral parts of biochemistry; however, heating concentrated aqueous amino acid solutions or heating amino acids in the dry state can give rise to peptides of various molecular weights depending on the conditions of synthesis. In addition to the biological amino acids, abiotic synthesis may give rise to a variety of nonbiological amino acids, including N-substituted and β- and α,α-disubstituted amino acids, among other types, some of which are found in contemporary organisms. It seems likely that abiotic synthesis provided some, but not all, of the coded amino acids in addition to many not found in coded proteins. Life’s use of the canonical 20 coded amino acids is thus likely the result of a protracted period of biological evolution. That this occurred in the context of biological systems is also likely because of the difficulty of stringing amino acids together abiotically to form long polypeptide chains. Once sufficiently robust oligomerization mechanisms were available, life would have been free to explore the combinatorial catalytic peptide space this innovation allowed access to.

There was no life yet, and even if, why would life have had the goal to explore catalytic peptide space ??

Fixation of Nitrogen in the Prebiotic Atmosphere 10
9 MARCH 1979
Reactions between nitrogen and water in the air surrounding lightning discharges can provide an important source of nitric oxide even under conditions where oxygen is a minor atmospheric constituent. Estimates are given for the associated source of soluble nitrite and nitrate. It is shown that lightning and subsequent atmospheric chemistry can provide a source of nitrate for the primitive ocean as large as 10.000.000 tons of nitrogen per year, sufficient to fill the ocean to its present level of nitrate in less than 10.000.000 years. The almost inevitable segregation of reduced and oxidized compounds between atmosphere and ocean could have implications for the emergence of primitive biology and should be considered in more complete models for atmospheric evolution.

Limits on Oxygen Concentration in the Prebiological Atmosphere and the Rate of Abiotic Fixation of Nitrogen 11
FEBRUARY 20, 1981
Dead organic material is depleted in nitrogen and phosphorus by roughly a factor of 2, so that the actual removal rate of Nitrogen atoms may be only about 2.5 x 10^9 cm -2 s. Nonetheless, this figure is still a factor of 10 higher than our estimated source of fixed nitrogen from the primitive atmosphere. Thus, there is every reason to suspect that a biological capacity for nitrogen fixation would have been a valuable and needed commodity even on the relatively oxygenic case 2 earth. 

A possible nitrogen crisis for Archaean life due to reduced nitrogen fixation by lightning 12
5 JULY 2001
Nitrogen is an essential element for life and is often the limiting nutrient for terrestrial ecosystems. As most nitrogen is locked in the kinetically stable form, N2, in the Earth's atmosphere, processes that can fix N2 into biologically available forms, such as nitrate and ammonia, control the supply of nitrogen for organisms. On the early Earth, nitrogen is thought to have been fixed abiotically, as nitric oxide formed during lightning discharge. The advent of biological nitrogen fixation suggests that at some point the demand for fixed nitrogen exceeded the supply from abiotic sources, but the timing and causes of the onset of biological nitrogen fixation remain unclear. Here we report an experimental simulation of nitrogen fixation by lightning over a range of Hadean (4.5±3.8 Gyr ago) and Archaean (3.8±2.5 Gyr ago) atmospheric compositions, from predominantly carbon dioxide to predominantly dinitrogen (but always without oxygen). We infer that, as atmospheric CO2 decreased over the Archaean period, the production of nitric oxide from lightning discharge decreased by two orders of magnitude until about 2.2 Gyr. After this time, the rise in oxygen (or methane) concentrations probably initiated other abiotic sources of nitrogen. Although the temporary reduction in nitric oxide production may have lasted for only 100 Myr or less, this was potentially long enough to cause an ecological crisis that triggered the development of biological nitrogen fixation.

Because biological nitrogen fixation is energetically expensive and does not occur if adequate supplies of fixed nitrogen are available, it has been generally thought that the development of metabolic pathways to fix nitrogen arose only in response to a crisis in the supply of fixed nitrogen on the early Earth. This sudden reduction may have occurred soon after the origin of life 7±10 as the prebiotic source of organic material was depleted by the emerging life forms. Our results suggest that the development of biological nitrogen fixation arose in response to changes in atmospheric composition that resulted in a reduction in the production of abiotically fixed nitrogen. The biochemistry of the nitrogen-fixing process, in particular, its sensitivity to oxygen, may reflect the timing of the nitrogen crisis and illustrates the co-evolution of the metabolic pathways in life and the environment of the early Earth.

Abiotic Nitrogen Fixation on Terrestrial Planets: Reduction of NO to Ammonia by FeS 13
Astrobiology, 2012
Understanding the abiotic fixation of nitrogen and how such fixation can be a supply of prebiotic nitrogen is critical for understanding both the planetary evolution of, and the potential origin of life on, terrestrial planets. As nitrogen is a biochemically essential element, sources of biochemically accessible nitrogen, especially reduced nitrogen, are critical to prebiotic chemistry and the origin of life. Loss of atmospheric nitrogen can result in loss of the ability to sustain liquid water on a planetary surface, which would impact planetary habitability and hydrological processes that shape the surface. It is known that Ntric Oxyde ( NO ) can be photochemically converted through a chain of reactions to form nitrate and nitrite, which can be subsequently reduced to ammonia. Here, we show that NO can also be directly reduced, by FeS, to ammonia. In addition to removing nitrogen from the atmosphere, this reaction is particularly important as a source of reduced nitrogen on an early terrestrial planet. By converting NO directly to ammonia in a single step, ammonia is formed with a higher product yield (*50%) than would be possible through the formation of nitrate/nitrite and subsequent conversion to ammonia. In conjunction with the reduction of NO, there is also a catalytic disproportionation at the mineral surface that converts NO to NO2 and nitrous oxide  ( N2O ). The NO2 is then converted to ammonia, while the N2O is released back in the gas phase, which provides an abiotic source of nitrous oxide.

Nitrogen is an essential element for life as we know it, and without it, key compounds in biochemistry, such a proteins, RNA, and DNA, would not be possible. For the origin and early evolution of life, an abiotic source of biochemically accessible nitrogen, especially reduced nitrogen, is necessary. Also, the abiotic fixation of nitrogen on terrestrial planets can have an enormous impact on the habitability and evolution of a planet. For example, loss of atmospheric nitrogen can lower atmospheric pressure and leave a planet unable to support liquid water. This leaves the surface of the planet unable to support life, and a lack of a hydrological cycle has an important effect on how the surface is, or is not, reshaped. The importance of understanding the nitrogen chemistry of terrestrial planets is clear, pathways that allow nitrogen to be converted to ammonia could have caused nitrogen to become sequestered in clay minerals Such formation of reduced ammonium would also have provided a source of nitrogen for prebiotic chemistry and for the formation of life.  Nitrogen fixation by atmospheric shock heating and subsequent chemistry is one important route for nitrogen fixation. On terrestrial planets with a nonreducing atmosphere that is, a CO2/N2 atmosphere with little or no carbon monoxyde CO and hydrogen gas H2, shock heating leads to NO formation. Thus, chemical routes that fix NO into forms that are chemically accessible for the origin of life or into forms that become sequestered into the crust become important. It is known that NO can become photochemically converted to nitrate and nitrite, which can subsequently be reduced to ammonia. Since both nitrate and nitrite can be reduced by iron(II), in the form of FeS, we became interested in whether FeS could lead to the direct reduction of NO to ammonia. The direct reduction of NO could be the most direct route to convert NO to reduced nitrogen.

That would still remain open, how FE/S clusters formed abiotically on earth, and the subsequent evolutionary route of ultracomplex biosynthesis of nitrogenase enzymes. 

1. https://www.researchgate.net/publication/242865828_Chemical_evolution_and_ammonia_in_the_early_Earth%27s_atmosphere
2. http://www.els.net/WileyCDA/ElsArticle/refId-a0000628.html
3. https://hazen.carnegiescience.edu/sites/default/files/186-ElementsIntro.pdf
4. ASTROBIOLOGY An Evolutionary Approach, page 100
5. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060018
6. https://www.nature.com/articles/365630a0
7. GENESIS - IN THE BEGINNING, Cellular Origin, Life in Extreme Habitats and Astrobiology Volume 22, page 204
8. http://sci-hub.hk/https://www.nature.com/articles/238268a0
9. http://sci-hub.hk/https://www.sciencedirect.com/science/article/pii/001910357990126X
10. http://sci-hub.hk/http://science.sciencemag.org/content/203/4384/1002
11. http://sci-hub.hk/http://onlinelibrary.wiley.com/doi/10.1029/JC086iC02p01147/full
12. http://sci-hub.hk/https://www.nature.com/articles/35083537
13. http://sci-hub.tw/10.1089/ast.2011.0646



Last edited by Admin on Thu Mar 29, 2018 9:53 am; edited 5 times in total

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The availability of  ammonia on early earth, a major hurdle to explain the origin of life

In order for matter to arrange itself into form, complexity, and ultimately, life, the necessary basic building compounds had to be readily extant, available and concentrated for the prebiotic chemical interactions to begin on early earth. One of the essential building blocks required were nitrogen in the form of either ammonia, nitrite, or nitrate. Today, microorganisms employ extremely complex and sophisticated biosynthesis pathways to transform nitrogen gas in the atmosphere into ammonia, and the atmospheric nitrogen cycle maintains everything in balance.  On a prebiotic earth, nitrogen-fixing bacterias were not extant. The availability of ammonia is amongst many other compounds an essential question to be answered by the origin of life researcher community, and several science papers were dedicated to elucidating this question. The result of these investigations is as follows:

The lifetime of ammonia (NH3) would be short because of its photochemical dissociation. The initial ammonia NH3 mixing ratio was 10-4 then in only 40 years, the NH3 would have been destroyed through photolysis. If the mixing ratio were 10-5, then the lifetime was less than 10 years.

Another paper reports: any ammonia present would have been photolyzed in 30000 years or less by UV light. (  Photolysis, the chemical process by which molecules are broken down into smaller units through the absorption of light. )

Another problem is - even if it would be supposed that ammonia accumulated on earth:

" the actual removal rate of Nitrogen atoms may be only about 2.5 x 10^9 cm -2 s. Nonetheless, this figure is still a factor of 10 higher than our estimated source of fixed nitrogen from the primitive atmosphere. Thus, there is every reason to suspect that a biological capacity for nitrogen fixation would have been a valuable and needed commodity even on the relatively oxygenic case to earth."

So what did they do ? - after all, Life is here, God is a non - answer, so let's make things up !!   So, realistic - or not, let's figure out and invent a "possible"  scenario - Science magazine reports:

http://sci-hub.hk/http://science.sciencemag.org/content/203/4384/1002

" Reactions between nitrogen and water in the air surrounding lightning discharges can provide an important source of nitric oxide even under conditions where oxygen is a minor atmospheric constituent. Estimates are given for the associated source of soluble nitrite and nitrate. It is shown that lightning and subsequent atmospheric chemistry can provide a source of nitrate for the primitive ocean as large as 10.000.000 tons of nitrogen per year, sufficient to fill the ocean to its present level of nitrate in less than 10.000.000 years."  

Wow - problem solved - apparently. But now, automatically, another hard nut  had to be cracked:

If lightning was and is a sufficient mechanism to transform nitrogen gas into nitrite and nitrate, the nitrogen form that organisms can uptake in liquid form for biological use - why did diazotrophs ( nitrogen-fixing bacterias ) like Cyanobacteria, and later, rhizobia, which live in nodules on the roots of legumes, some woody plants etc., and form a convenient symbiosis - came up with an extremely sophisticated biosynthesis pathway to transform dinitrogen into ammonia - and put 'extremely complex" to that !!??

and so the sciency storytelling goes:

First, there was ammonia on early earth, readily available through lightning, which permitted the first chemical reactions to form the basic building blocks of life, amino acids, RNA, DNA etc., and life emerged and kept replicating- until: " atmospheric CO2 decreased over the Archaean period, the production of nitric oxide from lightning discharge decreased by two orders of magnitude until about 2.2 Gyr.  Although the temporary reduction in nitric oxide production may have lasted for only 100 Myr or less, this was potentially long enough to cause an ecological crisis that triggered the development of biological nitrogen fixation. Because biological nitrogen fixation is energetically expensive and does not occur if adequate supplies of fixed nitrogen are available, IT HAS BEEN GENERALLY THOUGHT  that the development of metabolic pathways to fix nitrogen arose only in response to a crisis in the supply of fixed nitrogen on the early Earth.   This sudden reduction may have occurred soon after the origin of life 7±10 as the prebiotic source of organic material was depleted by the emerging life forms. Our results suggest that the development of biological nitrogen fixation arose in response to changes in atmospheric composition that resulted in a reduction in the production of abiotically fixed nitrogen. The biochemistry of the nitrogen-fixing process, in particular, its sensitivity to oxygen, may reflect the timing of the nitrogen crisis and illustrates the co-evolution of the metabolic pathways in life and the environment of the early Earth.

Now, this is a prime example of baseless storytelling, based just on guesswork and evidence lacking suppositions. Let us give a more detailed analysis of what they just told us: Nitrogenase requires electrons. The electron supply comes from photosynthesis which generates oxygen. Oxygen produces hydroxyl radicals.    

To avoid their DNA getting wrecked by hydroxyl radicals that naturally occur in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. Nick Lane brings it to the point:   Before cells could commit to oxygenic photosynthesis, they must have learned to deal with its toxic waste, or they would surely have been killed. But how could they adapt to oxygen if they were not yet producing it?

It's difficult to fathom how the protective mechanisms could have emerged gradually, since, while not fully operating, the bacterias would have been killed. 

Nick Lane admits: An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favor such a catastrophic history. In terms of the traditional account of life on our planet, the difficulty and investment required to split water and produce oxygen is a Darwinian paradox.

Many cyanobacterial species are capable of nitrogen fixation. However, oxygenic photosynthesis and nitrogen fixation are incompatible processes because nitrogenase is inactivated by oxygen. Cyanobacteria mainly use two mechanisms to separate these activities: a biological circadian clock to separate them temporally, and multicellularity and cellular differentiation to separate them spatially.

Both processes had to be fully developed and operational right from the beginning, there is no way they could have evolved gradually.

Within legume root nodules, rhizobia differentiate into bacteroids that oxidize host-derived dicarboxylic acids, which is assumed to occur via the tricarboxylic acid (TCA) cycle to generate NAD(P)H for reduction of nitrogen.

So, ultimately, the electrons are supplied by the host, namely plants, which, however, in the evolutionary narrative, emerged much later than cyanobacteria, that is, plants are supposed to evolve about 800 Mio years ago, while Cyanobacteria are much older, up to 3 billion years old, belonging to the most ancient organisms known. Now, let's return to the supposition, that nitrogenase evolved as consequence of ammonia shortage. It would have to be considered and analyzed, how the entire biosynthesis pathway of nitrogen fixation emerged. 

Nitrogen fixation is not a trivial task, but one of the most energy demanding processes in biological systems, made possible by nitrogenase enzymes, a complex molecular machine made of two main subunits and 3 metal clusters,  which are essential for catalysis, and  amongst the most complex made by nature, and performing an "optimal reaction".   A minimum of eight association/ dissociation events is required by the two subunits, for each Nitrogen N2 reduced. Why would evolutionary pressures develop any of the intermediate stages, if only after eight cycles, enough electrons are supplied, to split nitrogen? Furthermore:  If any of the co-factors, apo-proteins, or sub-units is missing, the enzyme cannot catalyze any reaction. Also - if there is no external supply of electrons, and energy in the form of ATP, coming from ferredoxin, and ultimately, from photosynthesis, no deal, no reaction, no nitrogen fixation. This makes the whole system irreducible and interdependent - the hallmark of intelligent design. Such systems could not emerge gradually by natural selection, or genetic drift, since:

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.

The task of Nitrogenase enzymes, called " the molecular sledgehammer",  is enormous: Dinitrogen is one of the least reactive compounds found in nature. This is because of the very high strength of its triple, N≡N, bond. This gives it a very high dissociation energy (at 3,000°C, at standard pressure, there is no significant dissociation) and makes chemical interactions with its p system (electrons involved in the triple bond) very weak. The alternative mechanism is through lightning. The first step in atmospheric chemistry to fix nitrogen involves processes such as lightning and meteors. These produce very high temperatures, >10,000 K.  The products of such heating depend on the composition of the atmosphere being shocked.

Availability of ammonia in a prebiotic earth
http://reasonandscience.heavenforum.org/t2689-availability-of-ammonia-in-a-prebiotic-earth

Overview of the Nitrogenase enzyme complex
http://reasonandscience.heavenforum.org/t2590-origins-what-cause-explains-best-our-existence-and-why#5867

The naturalistic narrative simply does not withstand scrutiny. Neither is there clear evidence that there was a consistent supply of Ammonia on early earth, a life-essential pre-requisite, and there is no evidence that there was enough supply through lightning. Neither is there evidence that there was a shortage of ammonia through the consumption of organisms on early earth, and neither that this shortage could have been the trigger for unicellular bacterias to develop the molecular nitrogen fixation process in a gradual manner, as evolutionary explanations demand. This evidence lines up to tons of others, which bury origin of life and biodiversity through evolution explanations, without a guiding intelligent and potent causal agent. 

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