Rethinking the Dawn of Life

Rethinking the Dawn of Life: Were We 

Wrong About How It All Began?

Here is an article I have read.

https://www.popularmechanics.com/science/a69137600/amino-acids-origin-of-life-order-wrong/

Scientists Say We May Have Been

Wrong About the Origin of Life

That was an excellent article I read that touches on one of the deepest and most fascinating scientific and philosophical questions: how life first began from non-living matter.

Having read that article, let me now give and share my personal thoughts with a summary view that reflects both the scientific shift and a broader philosophical view here: 

In a peer-reviewed analysis, scientists

quantify amino acids before and after 

our “last universal common ancestor.” 

The last universal common ancestor 

(LUCA) is the single life form that 

branched into everything since.

Earth four billion years ago may help us 

check for life on one of Saturn’s moons 

today. Scientists are making a case for 

adjusting our understanding of how 

exactly genes first emerged. For a 

while, there’s been a consensus about 

the order in which the building-block 

amino acids were “added” into the box 

of Lego pieces that build our genes. But 

according to genetic researchers at the 

University of Arizona, our previous 

assumptions may reflect biases in our 

understanding of biotic (living) versus 

abiotic (non-living) sources. In other 

words, our current working model of 

gene history could be undervaluing 

early protolife (which included 

forerunners like RNA and peptides), as 

compared to what emerged with and 

after the beginning of life. Our 

understanding of these extremely 

ancient times will always be incomplete, 

but it’s important for us to keep 

researching early Earth. The scientists 

explain that any improvements in that 

understanding could not only allow us to know more of our own story, but also 

help us search for the beginnings of life 

elsewhere in the universe. In this paper, 

published in the peer-reviewed journal 

Proceedings of the National Academy of 

Science, researchers led by senior 

author Joanna Masel and first author 

Sawsan Wehbi explain that vital pieces 

of our proteins (a.k.a. amino acids) 

date back four billion years, to the last 

universal common ancestor (LUCA) of 

all life on Earth. These chains of dozens 

or more amino acids, called protein 

domains, are “like a wheel” on a car, 

Wehbi said in a statement: “It’s a part 

that can be used in many different cars, 

and wheels have been around much 

longer than cars.” The group used 

specialized software and National Center 

for Biotechnology Information data to 

build an evolutionary (so to speak) tree 

of these protein domains, which were 

not theorized or observed until the 

1970s. Our knowledge of these details 

has grown by leaps and bounds. One

 big paradigm shift proposed by this

 research is the idea that we should 

rethink the order in which the 20 

essential genetic amino acids emerged 

from the stew of early Earth. The 

scientists argue that the current model 

overemphasizes how often an amino 

acid appeared in an early life form, 

leading to a theory that the amino acid 

found in the highest saturation must 

have emerged first. This folds into 

existing research, like a 2017 paper 

suggesting that our amino acids 

represent the best of the best, not just

 a “frozen accident” of circumstances. In 

the paper, the scientists say that amino 

acids could have even come from 

different portions of young Earth, rather 

than from the entire thing as a uniform 

environment. Tryptophan, the maligned 

“sleepy” amino found in Thanksgiving 

turkey, was a particular standout to the 

scientists (its letter designation is W). 

“[T]here is scientific consensus that W 

was the last of the 20 canonical amino 

acids to be added to the genetic code,” 

the scientists wrote. But they found 

1.2% W in the pre-LUCA data and just 

.9% after LUCA. Those values may 

seem small, but that’s a 

25% difference. 

Why would the last amino acid to 

emerge be more common before the 

branching of all resulting life? The team 

theorized that the chemical explanation 

might point to an even older version of

the idea of genetics. As in all things 

evolutionary, there’s no intuitive reason 

why any one successful thing must be 

the only one of its kind or family to ever 

exist. “Stepwise construction of the 

current code and competition among 

ancient codes could have occurred 

simultaneously,” the scientists conclude. 

And, tantalizingly, “[a]ncient codes 

might also have used noncanonical 

amino acids.” These could have

emerged around the alkaline

hydrothermal vents that are believed to 

play a key role in how life began, 

despite the fact that the  resulting life 

forms did not live there for long. To 

apply this theory to the rest of 

the universe, we don’t have to go far, 

either. “[A]biotic synthesis of aromatic 

amino acids might be possible in the 

water–rock interface of Enceladus’s 

subsurface ocean,” the scientists 

explain. That’s only as far as Saturn. 

Maybe a Solar System block party is 

closer than we think.

 Having written that, let me think again to offer my other alternative view here. 

For decades, scientists have sought to piece together one of the most profound mysteries in science, how life first arose from the lifeless chemistry of early Earth. Our prevailing models, though ingenious, may now be showing cracks. A recent study from researchers at the University of Arizona, published in the Proceedings of the National Academy of Sciences (PNAS), challenges the long-held assumptions about the order in which amino acids, the fundamental building blocks of proteins - emerged in the primordial world.

A New Look at Life’s Ancient Blueprint

Every living organism today, from a bacterium to a human, descends from what scientists call the Last Universal Common Ancestor (LUCA) - a single, ancient life form that existed about four billion years ago. LUCA is not the first life form, but the branching point from which all known life diversified.

To reconstruct LUCA’s world, the Arizona researchers, led by evolutionary biologist Joanna Masel and her colleague Sawsan Wehbi, analyzed massive datasets from the National Center for Biotechnology Information (NCBI). Using specialized computational models, they mapped the evolution of protein domains,  recurring structures made up of amino acids, the “wheels” that can be reused across countless biological “vehicles.”

What they discovered was both surprising and humbling: our standard timeline of how amino acids appeared in the genetic code might be wrong.

Turning the Clock Sideways

Until now, most scientists believed that the 20 canonical amino acids entered life’s genetic code gradually,  from the simplest, earliest ones like glycine and alanine to the more complex ones like tryptophan (represented by “W”), thought to be the last added. But Masel’s team found evidence that some complex amino acids existed even before LUCA, earlier than expected.

For example, tryptophan, previously considered a latecomer - showed a higher proportion in pre-LUCA data (1.2%) than after LUCA (0.9%). Though the difference seems small, it represents a 25 percent shift, enough to suggest that our chemical ancestry might have been far more diverse before life “standardized” into the familiar genetic code we know today.

This discovery implies that the early Earth may have hosted multiple genetic systems or “codes” competing for survival. Life as we know it could be the winner of an ancient biochemical competition, rather than a product of one continuous linear evolution

The Chemistry Before Biology

The implications go even deeper. The study suggests that proto-life,  chemical systems that were not yet alive but already self-organizing, may have experimented with different amino acid sets and coding systems before one became dominant.

This aligns with the idea that the boundary between “non-living” and “living” matter was not a single spark, but a gradual chemical awakening,  a transition from self-replicating molecules like RNA and peptides toward what we now call life.

If so, then our current understanding may be biased, viewing life’s history through the lens of biology rather than prebiology, and thereby underestimating the creative potential of chemistry itself.

Echoes Beyond Earth

Perhaps the most exciting part of this reinterpretation is its cosmic implication. If life’s earliest amino acids were not strictly “biotic,” then similar chemistry could easily occur elsewhere. Saturn’s icy moon Enceladus, with its subsurface ocean and hydrothermal vents, could host the same chemical playground where amino acids first formed.

Indeed, Masel and her colleagues propose that abiotic synthesis of complex amino acids might still be happening there today. This means the chemical prelude to life might be a universal process, not confined to Earth, but scattered across the cosmos, awaiting the right conditions to awaken into biology.

A Philosophical Reflection

If the scientists are right, then life was not a miraculous event that occurred once and by chance,  but a natural outcome of the universe’s inherent tendency toward complexity, organization, and self-awareness.

Yet, one cannot help but marvel: what invisible intelligence or cosmic order allowed inert atoms to assemble into thinking beings capable of asking such questions? Whether one sees it as divine design or as nature’s own deep law, the mystery remains equally profound.

As the researchers themselves suggest, we may never fully reconstruct that ancient moment of genesis. But every discovery - every reordering of amino acids or decoding of LUCA’s secrets, brings us closer to understanding the continuum between matter and mind, chemistry and consciousness, creation and Creator.

And perhaps, somewhere under the icy crust of Enceladus or in another corner of the universe, another form of life is asking the same question about us.

Here are some key references to support mpersonal thoughts in our discussions,  studies on the Last Universal Common Ancestor (LUCA), the genetic code and amino-acid recruitment, as well as broader origin-of-life context".  

Reference: 

I’ve selected a mix of primary peer-review papers and review articles.

Primary research

1. Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains — Sawsan Wehbi, Andrew Wheeler, Benoît Morel et al., Proceedings of the National Academy of Sciences (PNAS). The paper directly addresses the order in which the canonical amino acids entered the genetic code via domain-level phylogenomics. PNAS+2PNAS+2

DOI: 10.1073/pnas.2410311121 PNAS

This is the paper underlying the findings you read about (amino-acid frequencies pre- and post-LUCA). 

2.The nature of the last universal common ancestor and its impact on early evolution — A recent review (published 2024) on LUCA and what it tells us about early life. Nature Ecology & Evolution. Nature+1

3. Review & conceptual context

The Future of Origin of Life Research: Bridging DecadesOld Divisions — De Vladar H.P. (2020?); this review discusses various origins-of-life models including amino acids, peptides, RNA worlds, etc. Key for context on prebiotic chemistry and the origin of the genetic code. PMC

4. For the origin and definition of LUCA: All Life on Earth Today Descended From a Single Cell. Meet LUCA. — a more popular-science style but still backed by primary sources. Quanta Magazine

Additional reading suggestions

5. On amino-acid recruitment and genetic code evolution: Knight R.D., Freeland S.J., Landweber L.F., Selection, history and chemistry: the three faces of the genetic code, Trends in Biochemical Sciences (1999). PMC+1

On alternative amino-acid sets / xeno-biochemistry: Xeno Amino Acids: A look into biochemistry as we don’t know it - Brown S.M., Mayer-Bacon C., Freeland S. (2023) (arXiv preprint) exploring how non-canonical amino acids might feature in alternative biochemistries. arXiv

 

Voyagers of the Eternal Night: A Journey Through the Silent Oceans of Space

Thirty years ago I gave a talk on Space Travel at the National Science Centre in Kuala Lumpur on behalf of the Malaysian Senior Scientists Association (MSSA) at the invitation of Senior Academician Emeritus Professor Tan Sri Dato Dr Augustine SH Ong who then was the Founder and President of MSSA.  

Surprisingly, it was very crowded, and among them, far at the back of the auditorium I spotted an old friend of mine - Captain Lim Khoy Hing who was then an airline captain flying the Boeing 777 with MAS, and later with AirAsia on Airbus A320, AirAsia X A330/A340 . He was sitting there quietly listening to my "judo argument" or rather an intellectual discourse the horrendous hurdles of humans attempting space flights to another world

 

Today, 30 years later, I still remember some of the highlights

in my presentation at the National Science Centre. I then

 decided to write a more detailed account of my thoughts then, and break them into 6 parts for easier reading to

 dedicate them to Captain KH Lim after reading his

 interesting account  two days ago about  having robots to

 pilot future aircrafts here:   

 

https://askcaptainlim.com/pilotless-commercial-passenger-aircraft-is-it-a-bad-idea/

 

Below is just part 5 of my 6 parts article on space travels.

https://scientificlogic.blogspot.com/search?q=space+travel

Readers need to continue to scroll down for the rest of the 1 to 6 parts. All six  parts are devoted to Captain KH Lim. I hope he enjoys it along with the rest of my gentle readers  

The Fuel Required by Giant and a Human Being

 

This article is dedicated to  Captain Lim Khoy Hing, a retired Senior Pilot with MAS flying the AirAsia Airbus A320, AirAsia X A330/A340 and the Boeing 777 with Malaysia Airline. 

Captain Lim is an old friend of mine of many years, and I told  him  actually  I 

wanted to be a either a pilot, an astronomer, a physicist or a mathematician, but not  a doctor or a biological and a medical research  scientist.  

Here I am writing my thoughts not as a pilot for which I am not, but as a nutritionist since both  an aircraft and the human body require fuel to function   

“Fueling Giants and Fueling Humans: A Tale of Power, Energy, and the Flight of a Boeing 737” like the Tales of Two Cities by Charles Dickens. 

An Essay on Jet Engines, Human Metabolism, and the Shared Language of Energy

Since the dawn of aviation, few machines have left a deeper imprint on global travel than the Boeing 737. First introduced in the late 1960s, this narrow-body, twin-engine jet soon became the best-selling commercial aircraft in history. Today, it remains the workhorse of airlines across continents, taking millions of travelers to their destinations every day.

But behind its familiar silhouette lies a story of power, physics, and energy, one that intriguingly mirrors the way the human body itself uses fuel.

The Boeing 737: A Compact Giant of the Skies

Modern variants such as the Boeing 737-800 and 737 MAX 8 operate at a Maximum Takeoff Weight (MTOW) of:

≈ 79,000 kg for the 737-800

≈ 82,600 kg for the 737 MAX 8

Each engine of a 737-800,  typically a CFM56-7B,  can produce up to 27,300 pounds of thrust, though everyday takeoffs often use lower thrust settings to prolong engine life. The MAX 8 engines push even further, delivering a combined thrust approaching 249 kN (≈ 56,000 lbf).

In terms of raw power, the two engines together develop the equivalent of 15–20 megawatts (MW) during takeoff — roughly 20,000 to 27,000 horsepower. This is the muscle needed to lift an 80-tonne machine into the sky.

Jet Fuel: The “Food” That Powers an Aircraft

Just as the human body thrives on carbohydrates, fats, and proteins, jet engines depend on their own form of food: kerosene-based aviation fuel.

Jet A vs Jet A-1

Jet A - used primarily in the United States

Jet A-1 - used globally due to its lower freezing point (–47°C vs –40°C)

For most Boeing 737s, Jet A-1 is the predominant fuel

Energy Content of Aviation Fuel

Aviation kerosene contains approximately:

43.1 megajoules per kilogram (MJ/kg)

≈ 12 kWh per kg

This extremely high energy density is what allows a relatively small mass of fuel to produce enormous power.

To illustrate:

580 kg of jet fuel = ~25 gigajoules of energy
(580 kg × 43.1 MJ/kg = 24.998 GJ)

That is the same amount of energy a typical Malaysian home might consume in eight months.

How Much Energy Does Takeoff Really Require?

The power of a jet engine is usually described by thrust, but converting thrust to energy reveals the scale of what happens during takeoff.

During the takeoff and initial climb to 10,000 feet (3,048 metres),  a process lasting several minutes, a Boeing 737-800 typically uses about:

≈ 580 kg of fuel ≈ 6,960 kWh (≈ 25 GJ) of energy

This includes the takeoff roll (usually less than 1 minute), the climb to 10,000 ft (often 11–20 minutes)

Importantly, only a small fraction of the 580 kg is consumed on the runway itself. Most of it is burned during the sustained high-power climb.

In broader flight operations, industry sources estimate:

≈ 2,300 kg of fuel (about 700 gallons) is used from takeoff to the first 3,000 ft of altitude across an average flight profile.

At full takeoff thrust, each engine may burn 2,200–2,700 kg of fuel per hour.

Environmental factors such as temperature, runway length, headwinds, and aircraft weight also significantly influence fuel burn.

Energy and Humans: A Comparison We Rarely Make

As a nutritionist, let me extend the analogy between aircraft fuel and human food energy; indeed, they share the same fundamental unit: the joule.

The daily energy requirement of an average adult human is remarkably small when placed beside the energy appetite of a jet engine.

Daily Human Energy Needs

Humans typically require:

0.150–0.250 MJ per kilogram of body weight per day. For example:

A 70-kg moderately active man requires
≈ 11.7 MJ/day (0.167 MJ/kg/day)

A 55-kg moderately active woman requires
≈ 10.1 MJ/day (0.183 MJ/kg/day)

These numbers depend on:

Basal Metabolic Rate (BMR), namely, the energy needed at complete rest.

Physical Activity Level (PAL) from 1.4 (sedentary) to >2.4 (very active)

In contrast, a Boeing 737 consumes 25,000 MJ just to climb to 10,000 feet — the equivalent of the entire daily caloric needs of 2,137 adult men in a single ascent.

The Shared Language of Life and Machines

Despite their differences, the human body and a jet airliner obey the same universal physics:

Both convert chemical potential energy into motion. Both operate within limits of efficiency. Both require specialized fuel. And both must balance power output with structural and thermal constraints.

What differs is scale. A human body may burn the caloric energy of a banana to climb a flight of stairs; a Boeing 737 burns nearly half a tonne of kerosene to climb into the sky.

Yet the underlying principle remains beautifully the same:
Energy becomes lift, motion, and life.

Conclusion:

Understanding the fuel needs of 

a Boeing 737 opens a window into the 

astonishing power of modern 

engineering. And comparing this with 

human metabolic needs reveals a poetic 

symmetry  from the beating heart to

the  roaring turbofan, the laws of

energy  bind us all.

The Law of Parity in Physics

The Law of Symmetry in Physics

 

by: lim ju boo (lin ru wu)  

Recently, the world lost one of the most important scientific personality - James Dewey Watson (April 6, 1928 – November 6, 2025) an American molecular biologist, geneticist, and zoologist who died at the age of 97. 

In 1962, Watson, Crick, and Maurice Wilkins were awarded the Nobel Prize in Physiology or Medicine for their discoveries concerning the molecular structure of nucleic acids -deoxyribonucleic (DNA) and its significance for information transfer in living material. 

I have written quite a lot of articles here on molecular biology, DNA and also its applications in medicine, forensic science, agriculture among others, and I shall not repeat them here.  

In this year (2025) alone, we also lost another Nobel Prize winners - Yang Chen-Ning who won the Nobel Prize in physics in 1957, 

I shall today write an article on physics instead concerning Yang Chen-Ning. 

I received this piece of news on the demise of China's first Nobel laureate, Yang Chen-Ning

https://www.chinadaily.com.cn/a/202510/18/WS68f3170ea310f735438b5bf2.html

I heard about this first Chinese scientist who won the Nobel Prize in Physics in 1957 from my classmate when I was only in Form 4 in school, and naturally, I could not understand  what this theory of parity was all about till I studied physics and mathematics in a university years  later.

Friends and former colleagues of mine who are medical doctors have not much clue in physics or chemistry are also now asking me what is this theory of parity all about?

The theory of parity non-conservation is the principle that some subatomic particle interactions, specifically the weak nuclear force, are not mirrored in a mirror image. "Parity" is the physics concept of mirror symmetry, and before the work of Yang and Lee, it was believed that all physical laws were symmetric, meaning a process and its mirror reflection should behave identically. Yang and Lee proved this wasn't true for the weak interaction, a discovery that revolutionized physics by showing that a fundamental symmetry of nature was not universal. 

Parity symmetry: Think of a mirror. In a mirror, left and right are swapped, but up and down are not. Parity conservation was the idea that the laws of physics should hold true even if you viewed them in a mirror. For example, if you dropped a ball, its mirror image would also drop. This was thought to be a fundamental law for all forces.

Weak interaction: This is one of the four fundamental forces of nature, responsible for things like radioactive decay.

Yang and Lee's discovery: They theorized and later proved that the weak interaction is "chiral," meaning it is not mirror symmetric. This is like a left-handed glove not fitting a right hand. The weak force can distinguish between "left-handed" and "right-handed" particles, breaking the principle of parity conservation.

Impact: This discovery was a major breakthrough, upending a long-held assumption in physics. It demonstrated that the laws of nature are not universally symmetrical and led to a deeper understanding of elementary particles and the fundamental forces. 

Let me now explain this in another simpler way:  Understanding Parity - Using A Simple Idea and Life Illustrations.

 

Let me now explain them under this title:

When the Mirror Lied: Yang Chen-Ning and the Hidden Asymmetry of Nature

A Tribute to a Giant of Physics

On 18 October 2025, the world lost one of its greatest scientific minds - Professor Yang Chen-Ning (Yang Zhenning) who passed away peacefully in Beijing at the age of 103.

Born in 1922 in Anhui Province, China, Yang grew up during a turbulent era of war and political change but rose through hardship to become one of the most brilliant theoretical physicists of the 20th century.

After graduating from the National Southwest Associated University during wartime China, Yang later pursued his Ph.D. at the University of Chicago under the legendary physicist Enrico Fermi. In 1957, at the age of just 35, he and his colleague Tsung-Dao Lee became the first Chinese-born scientists to receive the Nobel Prize in Physics for their groundbreaking theory that parity is not conserved in weak nuclear interactions. This discovery fundamentally changed modern physics and reshaped our understanding of the universe.

What exactly did Yang discover that was so profound? To understand this, we must take a journey, not through complex mathematics or quantum jargon, but through simple observation, biology, and ordinary life which my gentle readers here can understand

Parity is nothing more than mirror symmetry. It asks a simple question:

Would the laws of nature still work if everything were flipped in a mirror - left becomes right and right becomes left?

For example, if a person kicks a football with their right leg, in the mirror it looks like they are kicking with their left, but the action still makes sense. So we’d say: football respects parity.

For over a century, physicists believed that all natural laws behaved this way, that nature does not care about left and right.

Yang and Lee challenged this belief, and they were right.

Biology Already Told Us: Nature Is Not Perfectly Symmetric

Even before physics discovered this, biology already knew that nature breaks mirror symmetry.

1. Our Bodies Are Not Mirror - Symmetric

If you look inside your body, your heart is slightly to the left, your liver mostly on the right, and even the two halves of your brain have different functions. If humans were perfectly symmetric, flipping us into a mirror would still make perfect biological sense, but it doesn’t.

2. Life Prefers One Hand

Chemically speaking, molecules can be left-handed or right-handed (a property called chirality). But all amino acids in living organisms are left-handed. The right-handed versions simply do not function in the body.

3. DNA Twists Only One Way

The DNA double helix twists in a right-handed spiral, never the mirror version in normal biology. Life has chosen a direction.

So symmetry is not universal. Nature often chooses one side over the other.

Yang and Lee’s Revolutionary Question

In the 1950s, there was a puzzle in nuclear physics called the tau-theta problem. Two particles that looked identical behaved differently, something strange was going on. Yang and Lee proposed a bold idea:

What if the weak nuclear force does not obey mirror symmetry (parity)?

This was unthinkable. It challenged decades of unquestioned belief in physics. Many dismissed the idea, but Yang and Lee persisted. They worked with experimental physicist Chien-Shiung Wu, and in 1957 she performed a brilliant experiment using cobalt-60, a radioactive isotope.

The results shocked the world:

The electrons emitted during radioactive decay did not go out evenly in all directions.
They preferred a specific direction.
 In the mirror version, this behavior would be impossible.

For the first time in history, science had proof:

Nature breaks mirror symmetry. Parity is violated in the weak nuclear force.

Simple Everyday Life Analogies to Understand 

Everyday / Biological Analogy	Meaning
Right-handed scissors don’t work well in the left hand	Nature doesn’t always treat left and right the same
Screws only turn in one direction	Some processes prefer a direction
Only left-handed amino acids work in life	Nature has a built-in preference
DNA twists in one direction	Symmetry is not absolute

The weak nuclear force is like this, it has handedness. It only interacts with left-handed particles, ignoring right-handed ones completely.

Why This Was So Important

Yang and Lee didn’t just answer a question in nuclear physics, they opened a door into a deeper truth about the universe:

1. Nature is not perfectly symmetric

2. The universe has structure and preferences

3. There are hidden rules still waiting to be discovered

Their discovery reshaped physics and helped build the Standard Model, our modern theory of fundamental particles.

Summary:  The Legacy of Yang Chen-Ning

Yang Chen-Ning taught the world a profound lesson—not only in physics but in thinking itself:

Never assume. Question even the most “obvious” truths.

His life’s work reminds us that science advances not by accepting tradition, but by challenging it boldly yet intelligently. Today, as we remember this towering figure of human thought, we honor not just a Nobel laureate, but a mind of courage, clarity, and curiosity who dared to ask a question the world had ignored.

And with that single question, he changed science forever.

Summary: 

The law of parity in physics, or conservation of parity, states that a physical system and its mirror image should behave identically, meaning nature is indifferent to left and right.  This law was long thought to apply to all fundamental interactions, but experiments in 1956 revealed that parity is violated in weak interactions (such as beta decay), though it remains conserved in strong interactions, electromagnetism, and gravity.