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