The Origin of Mystery of Life Itself (Part 2)

 

Just only yesterday I wrote out an essay to discuss the Origin of Life on Earth here:

https://scientificlogic.blogspot.com/2024/08/the-origin-of-life.html

But that hypothesis on LUCA, or the Last Universal Common Ancestor is generally acknowledged as the common ancestor of all living things. But that hypothesis does not tell us how LUCA became alive and living. I thought over this, and today I decided to answer this extremely difficult question being debated for centuries that has cracked the best scientific minds.

I hope with God’s guiding Hands I will be able to answer this mystery that has been hidden from us for such a long, long time, as long as we are physical and think only in physical terms that science dictates.

But first, let me bring you to the first 5 verses in the very, very beginning of time and creation themselves here:

 In the beginning God created the heavens and the earth.  The earth was without form, and void; and darkness was on the face of the deep. And the Spirit of God was hovering over the face of the waters.

Then God said, “Let there be light”; and there was light.  And God saw the light, that it was good; and God divided the light from the darkness.  God called the light Day, and the darkness He called Night.  So, the evening and the morning were the first day.

(Genesis 1:1-5)

This was how Earth was created according to Genesis in the Bible, but it did not specifically or directly say explicitly how life came into being. I shall go into these verses later. Bear with me. Let us first have a look at what science has to say.

In 1953 Miller-Urey carried out an experiment to stimulate the conditions of Earth’s early atmosphere and oceans to test whether organic molecules could be created abiogenetically, to mean to create life without life, but formed from chemical reactions occurring between inorganic molecules thought to be present at the time. Miller used discharged sparks inside his flask to simulate a lot of lightning over the primordial oceans when Earth was still void and very dark without light. I think he wanted to see if he could create those biochemical compounds pertaining to life based on his primordial soup theory.

The experiment—the results of which were published in the journal Science as “A Production of Amino Acids Under Possible Primitive Earth Conditions”—documented the production of amino acids and other organic molecules, thereby demonstrating that chemical evolution (that is, the formation of complex chemicals from simple ones) is possible. The Miller-Urey experiment is used as evidence to support hypotheses about the origins of life.

The Miller–Urey experiment was proof that the building blocks of life could be synthesized abiotically from gases and introduced a new prebiotic chemistry framework through which to study the origin of life. Simulations of protein sequences present in the last universal common ancestor (LUCA), or the last shared ancestor of all extant species today, show an enrichment in simple amino acids that were available in the prebiotic environment according to Miller-Urey chemistry. This suggests that the genetic code from which all life evolved was rooted in a smaller suite of amino acids than those used today.  

However, creationist argued that Miller–Urey experiments have not generated all 22 genetically-encoded amino acids.  But do these 22 genetically encoded amino acids actually conflict with the evolutionary perspective on the origin of life - “non-living origin” yes, but it did not insist they were life itself?  

Another common misconception is that the racemic (containing both L and D enantiomers) mixture of amino acids produced in a Miller–Urey experiment is also problematic for abiogenesis theories life on Earth because today the amino acids found in life are L-amino acids (left-handed amino acids). While it is true that Miller-Urey setups produce racemic mixtures, the origin of homochirality is a separate area in the origin of life research. I shall explain racemic mixtures, right-handed enantiomers (also called optical isomer, antipode, optical antipode) shortly.

The experiment used methane (CH₄), ammonia (NH₃), hydrogen (H₂), in ratio 2:2:1, and water (H₂O). Applying an electric arc to stimulate lightning believed to be the beginning of time when Earth was created, resulted in the production of amino acids.

In chemistry, a racemic mixture or racemate means one that has equal amounts of left- and right-handed enantiomers (also called optical isomer, antipode, optical antipode   of a chiral molecule or salt. Racemic mixtures are rare in nature, but many compounds are produced industrially as racemates.  In biology, 19 of the 20 natural amino acids are homochiral, being L-chiral (left-handed), while sugars are D-chiral (right-handed).

In 1848, French chemist Louis Pasteur discovered that some molecules essential for life exist in mirror image forms, much like our left and right hands. Today, we know biology chooses just one of these “chiral” forms: DNA, RNA, and their building blocks are all right-handed, whereas amino acids and proteins are all left-handed. Pasteur, who saw hints of this selectivity, or “homochirality,” thought magnetic fields might somehow explain it, but its origin has remained one of biology’s great mysteries.

When I first learn chemistry and biology in the university we were taught that  living biomolecules such as DNA, amino acids and sugars found in Nature are dextrorotatory isomer (Latin: dexter = right) or d-form, the optical isomer that spins plane polarised light to the right (clockwise) whereas those same synthetic analogues are mirror images of the life molecules on the left, namely, laevorotatory isomer, often known as I-form, the optical isomer that spins plane polarised light to the left (anticlockwise).

 But today having gone so far into chemistry and biochemistry I think there's a mix-up in the concepts related to the chirality of biomolecules. Let me explain.

Chirality in Biomolecules:

 In nature, the amino acids found in proteins are predominantly in the L-form (levo or left-handed), which corresponds to the L-configuration in their chiral centres. This is a convention rather than directly related to how they rotate plane-polarized light. Most natural L-amino acids are laevorotatory, but not all—some can be dextrorotatory. The L- and D- nomenclature is based on the molecule's relationship to glyceraldehyde's configuration rather than its optical activity.

Naturally occurring sugars, such as glucose, are generally found in the D-form (dextro or right-handed), which refers to their D-configuration at the chiral centre farthest from the carbonyl group. Again, this D-configuration doesn’t necessarily mean the sugar is dextrorotatory. For instance, D-glucose is dextrorotatory, but D-fructose is laevorotatory.

The building blocks of DNA, specifically the sugar component (deoxyribose), are in the D-form, consistent with other naturally occurring sugars.

The terms dextrorotatory (+) and laevorotatory (−) refer to the direction in which a substance rotates plane-polarized light, not directly to the D- or L- configurations.

A molecule in the D-configuration can be either dextrorotatory or laevorotatory, depending on its specific structure.

Synthetic molecules can be made as either the D- or L- form, and they can also be either dextrorotatory or laevorotatory. They are not necessarily mirror images of the natural molecules but can be produced in either form. Synthetic production can yield a racemic mixture (equal amounts of D- and L- forms), or it can be enantioselective, producing predominantly one form.

In other words, natural amino acids are generally in the L-form (which can be either dextrorotatory or laevorotatory). Natural sugars are usually in the D-form (which can be either dextrorotatory or laevorotatory). The optical activity (dextrorotatory or laevorotatory) is independent of the D- or L- configuration and depends on the specific structure of the molecule. Synthetic analogues can be produced in either D- or L- forms, and their optical activity can vary accordingly.

So, it's not true that all natural biomolecules are dextrorotatory or that their synthetic analogues are always laevorotatory; the relationship between structure and optical activity is more complex.

 Basic Elements of Life: 

The basic elements that compose DNA are five atoms: carbon, nitrogen, oxygen, phosphorus, and hydrogen. A nucleoside is the combination of these atoms into two structures, a five-carbon sugar molecule called deoxyribose, which is responsible for the name of DNA, and one of four nitrogen bases.

Amino acids are organic compounds containing amine [- NH2] carboxyl [-COOH] side chain [R group]. The major key elements of amino acids are carbon, hydrogen, nitrogen, oxygen. About 500 amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways

All these compounds are chemicals of life, but not life itself. They are dead molecules with no life in them, just life’s footprints. So, how did life infuse into them?

Having explained all the above based on our knowledge in biology and chemistry, let us now go back to the verses in Genesis.

Verses in Genesis: 

In verse 1, it says “In the beginning God created the heavens and the earth”. In verse 2, it clearly says the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.

But what does that 2^nd verse tell us implicitly?  I could instantly see it tells me that when all the essential biochemical compounds were created by lighting over the oceans as stimulated by Miller in his 1953 experiment but there was still no life in them. Whether in biology or in chemistry we know that no chemical, not even biomolecules have life into them that could cause them to automatically and mysteriously begin to move, respire, become sensitive and respond to stimuli, growth, reproduce, excrete and feed (nutrition) on their own. There must be something very much higher which I believe must be the soul or the spirit of God that commands these biological molecules to have life into them, meaning to be able to move, respire, sensitive, grow, reproduce, excrete and feed automatically on their own.

Having explained these characteristics and behaviour of life or something living, don’t we think it was the Spirit of God hovering over the waters of the oceans as clearly (to me) that caused all these molecules of life Miller simulated to spring alive?

Let us reinforce this with another verse

“And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul”

(Genesis 2:7). This verse clearly states that we need the breath of God, which translated, means His Spirit, which is the soul in our body – beyond the detection and measurement of science before the molecules can spring alive. The dust from the soil is not alive and can never be alive, not until God Himself breathes His spirit into them. This is so clear and acceptable to me as a researcher, a scientist and doctor. I do not know the rest of what they think.

Please accept and always remember that atoms and molecules are physical particles that are completely lifeless and non-living. They cannot move, respire or produce themselves on their own unless something unknown to science controls and orders them to do these. And that is the soul, the spirit, the ghost and God. Nothing else can do these miracles of life. Don’t you think I have got it right? Yes, or no?  

Not just that alone. In verse 1 in Genesis, it is clearly stated there was no light then.

“The earth was without form, and void; and darkness was on the face of the deep”

 This means there were no plants for photosynthesis then for other higher forms of life to evolve yet, except perhaps viruses, bacteria and simple microorganisms that do not require light. Scientists think the first type of photosynthesis that evolved did not produce oxygen. It was known to have first evolved around 3.5-3.8 billion years ago, but until now, scientists think that one of the groups of bacteria alive today that still uses this more primitive photosynthesis was the first to evolve with this ability.

It was through the emergence of embryophyte land plants that first occurs in the middle Ordovician (~470 million years ago), and by the middle of the Devonian (~390 million years ago) that have many of the features recognized in land plants today, including roots and leaves that may have produced an abundance of oxygen for other animals to emerge.

The church and scientists have been arguing and debating for centuries at loggerheads with each other on how life came into existence. As for me, my thinking with His guidance I believe may have solved all those mysteries

What’s your think? Explain clearly and logically to me.