Title: “The Breath Beyond Biology: Science, Soul, and the Mystery of Life

 This article is

 delicated to my

 brother-in-law

 Engineer Ong Geok

 Soo who always tell

 me there is no soul 

The Breath of Life Beyond Biology 

Since ancient times, philosophers and cultures across civilizations have believed in a vital force,  an invisible essence or energy that animates the living. This concept, known variously as the “vital force,” élan vital, prana, or qi, was seen as the mysterious current that separates the living from the non-living. Many traditions still uphold the belief that this force resides within the body and departs when life ends, leaving only a shell behind.

Modern science, however, dismisses the idea of such a non-physical “life energy.” It attributes life to the intricate interplay of chemistry and physics, to the organized dance of molecules, cells, and biochemical reactions. According to this view, life is not a mystical essence but an emergent property of complex systems capable of self-regulation, metabolism, and reproduction.

From Vitalism to Biochemistry

Vitalism once dominated biological thought. Its decline began in 1828, when German chemist Friedrich Wöhler synthesized urea, an organic compound, from inorganic materials. This landmark experiment shattered the notion that organic molecules required a “vital spark” from living organisms. Since then, molecular biology and biochemistry have demonstrated that all life processes, metabolism, growth, reproduction, and even consciousness, arise from intricate chemical and physical interactions obeying natural laws.

Urea is not life itself. It is merely an inert molecule, devoid of awareness, motion, or purpose. The puzzle remains: why do the same molecules that form a living being lose all vitality upon death?

When a person or animal dies, their DNA, proteins, and electrolytes remain initially intact. Chemically, little changes in the first moments after death, and yet the phenomenon we call life vanishes. The laws of chemistry alone do not fully explain why the same atoms arranged in the same way no longer sustain consciousness or motion. The “spark of life” seems to be more than the sum of its molecular parts.

The Unresolved Mystery of Death and Consciousness

Science explains death as the irreversible breakdown of physiological integration, the failure of circulation, respiration, and neural activity. Once homeostasis collapses, the system cannot self-regulate, and the organism ceases to live. Yet, this explanation still leaves a lingering question: what is the nature of the consciousness that departs when the brain stops functioning?

Accounts of near-death experiences (NDEs) challenge materialistic explanations. Individuals report traveling through dark tunnels, perceiving radiant light, or meeting deceased relatives in serene landscapes. More remarkably, some people born blind describe vivid visual scenes during NDEs, despite never having experienced sight.

Neuroscientists offer biochemical explanations: oxygen deprivation, endorphin release, or surges of neurotransmitters that cause hallucinations. However, such claims remain speculative. No ethically permissible experiment can measure real-time brain chemistry in dying individuals to confirm such theories.  The hypothesis of “chemical hallucination” is itself untested and untestable.

Science, Faith, and the Boundaries of Knowledge

At this frontier, we must recognize the limitations of science. Science investigates matter, energy, and forces, the observable and measurable. But not everything that exists must be measurable. As the philosopher Karl Popper noted, “Science may be said to be the art of the soluble,” it can only solve what lies within its methodological reach.

Concepts like the soul, spirit, or divine breath are non-physical by definition and therefore fall beyond the scope of scientific inquiry. The inability to measure them does not disprove their existence; it merely reflects the boundaries of our instruments and intellect. The absence of evidence is not evidence of absence.

The Scriptural Perspective

The Hebrew Scriptures give a profound metaphysical description of life’s origin. In Genesis 2:7 (KJV), it is written:

“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.”

This verse captures the union of the material and the immaterial — the dust of the earth and the divine breath. Similarly, Ephesians 6:12 reminds us that our struggles extend beyond the physical:

“For we wrestle not against flesh and blood, but against principalities, against powers… and against the spiritual forces of evil in the heavenly realms.”

Such passages remind us that not all realities are physical. Science may describe how life functions, but faith asks why life exists — and perhaps who breathes it into being.

Complementary Ways of Knowing

Science and spirituality need not be enemies. They are complementary ways of seeking truth. Science explores the mechanisms of creation; theology explores its meaning. As Albert Einstein himself said:

“Science without religion is lame; religion without science is blind.”

A mature worldview accepts that both are necessary — science to understand the structure of life, and faith to understand its purpose.

Conclusion

The mystery of life endures because it sits at the intersection of two domains: the measurable and the immeasurable, the temporal and the eternal. Science may one day decode the deepest workings of the cell, but whether it will ever grasp the essence of being alive, that invisible breath that transforms dust into a living soul - remains uncertain.

Perhaps, as I like to  conclude, humility is the truest mark of both science and faith. For in acknowledging our limits, we open the door to wonder, and to the possibility that life’s greatest truths may dwell not in the laboratory, but in the breath of God Himself.

Suggested References

1. Wöhler, F. (1828). Ueber künstliche Bildung des Harnstoffs. Annalen der Physik und Chemie.

2. Popper, K. (1963). Conjectures and Refutations: The Growth of Scientific Knowledge. Routledge.

3. Greyson, B. (2000). “Near-death experiences.” Journal of Scientific Exploration, 14(2), 233–256.

4. Beauregard, M., & O’Leary, D. (2007). The Spiritual Brain: A Neuroscientist’s Case for the Existence of the Soul. HarperOne.

5. Einstein, A. (1941). Science, Philosophy and Religion: A Symposium.

Veganism: Health Benefits, Limitations, and Global Acceptance

 

A Short Review on The Rise of the Vegan Diet: Health Benefits, Limitations, and Global Acceptance

A well-planned vegan diet, one that excludes all animal-derived foods, has moved from the fringes of nutrition science to the center of global health discussions. While its adoption worldwide remains relatively modest, rising awareness of chronic diseases, environmental sustainability, and animal welfare has drawn increasing attention to plant-based dietary patterns.

Scientific studies over the last two decades consistently show that a nutritionally balanced vegan diet can offer profound health benefits. At the same time, improper planning can lead to deficiencies with significant long-term consequences. This article explores the health advantages, growing acceptance, and potential risks of veganism, integrating current research findings and practical insights.

Health Benefits of a Well-Structured Vegan Diet

A whole-food, plant-based diet is naturally rich in dietary fiber, antioxidants, phytonutrients, vitamins, minerals, and unsaturated fats. These characteristics contribute to several well-documented health outcomes:

1. Weight Management and Metabolic Health

Numerous studies show that vegans have a lower average Body Mass Index (BMI) compared with omnivores. High-fiber, low-calorie-density foods promote satiety, making weight control more achievable without deliberate calorie restriction.

Supporting study:
– A 2015 meta-analysis in The Journal of the Academy of Nutrition and Dietetics found that individuals following vegan diets lost more weight than those on conventional weight-loss diets, even when eating until full.

2. Cardiovascular Protection

A vegan diet can improve lipid profiles and reduce risk factors for heart disease, including hypertension and inflammation.

Key findings:
– A 2019 review in Progress in Cardiovascular Diseases concluded that plant-based diets lower LDL cholesterol, reduce blood pressure, and significantly cut the risk of ischemic heart disease.
– High fiber intake reduces cholesterol absorption, while phytochemicals exert anti-inflammatory effects.

3. Prevention and Management of Type 2 Diabetes

Plant-based diets improve insulin sensitivity and glycemic control.

Supporting study:

- Research published in Nutrients (2020) showed that vegan diets reduced the risk of type 2 diabetes by up to 23%.

- The Physicians Committee for Responsible Medicine (PCRM) demonstrated that patients on a low-fat vegan diet achieved better HbA1c reduction than those on standard diabetes diets.

4. Reduced Cancer Risk

High consumption of vegetables, fruits, legumes, and whole grains is linked to a lower incidence of several cancers.

- The World Health Organization recognizes plant-based diets as protective against colorectal cancer.

- A 2022 study in BMC Medicine found that vegetarians and vegans have lower rates of colorectal, prostate, and breast cancers.

5. Enhanced Gut Health

The gut microbiome thrives on plant fiber, which acts as a prebiotic.

– Increased intake of fermentable fibers promotes beneficial bacteria such as Bifidobacteria and Lactobacilli.
– This microbial pattern is associated with lower inflammation, improved immunity, and better digestive function.

Global Acceptance and Adoption Trends

While veganism remains a minority lifestyle globally, interest is accelerating.

1. Global Prevalence

As of early 2020s estimates, about 79 million people identify as vegan, slightly over 1% of the world's population. However, millions more practice partial plant-based eating (flexitarianism).

2. Regional Variations

- United States: Approximately 2% identify as vegan, but up to 30% of young adults regularly choose plant-based alternatives.
- Israel: One of the highest global rates, estimated at 5–8%.
- India: Although most Indians are not vegan, vegetarianism is widespread due to cultural and religious influences, giving India a strong plant-forward dietary base.

3. Market Growth

The global plant-based food market is rapidly expanding.

– A 2021 Bloomberg Intelligence report predicts the plant-based food industry could reach US$162 billion by 2030, driven by health, environmental, and ethical motivations.

Disadvantages and Considerations

A vegan diet is not inherently healthy, it becomes beneficial only when properly planned. Several nutrients found abundantly in animal products must be obtained elsewhere:

1. Vitamin B12 Deficiency

Perhaps the most critical concern.
- B12 is essential for nerve function and red blood cell production.
- All vegans require B12 supplementation or consumption of fortified foods.

2. Iron

Plant-based iron (non-heme) is less bioavailable.
- Vegans require nearly double the recommended iron intake.
-  Pairing iron-rich foods with vitamin C increases absorption dramatically.

3. Omega-3 Fatty Acids

EPA and DHA, vital for brain and cardiovascular health, are scarce in plant foods.
- Algae-based supplements provide a reliable vegan source.

4. Calcium and Vitamin D

Low intake can harm bone density.

Study:

- A 2009 EPIC-Oxford cohort study found that vegans had a 30% higher fracture risk, largely due to inadequate calcium intake.

5. Protein, Zinc, and Iodine

While plant foods can provide these nutrients, vegans must plan carefully:

Protein: combine varied sources (soy, legumes, quinoa, nuts).
Zinc: found in beans, nuts, and whole grains but less absorbable.
Iodine: often requires iodized salt or supplementation.

6. Social and Practical Challenges

Dining out, family meals, and cultural norms may present obstacles. Some vegans report feelings of isolation in social settings dominated by animal-based dishes.

7. Mental Health Associations

Some studies suggest higher rates of anxiety or depression among vegans, although results are inconsistent and confounded by lifestyle, pre-existing mental health conditions, and ethical distress.

A vegan diet can be extraordinarily beneficial when executed thoughtfully. It excels in disease prevention, inflammation reduction, and metabolic health. However, it is not automatically healthier than other balanced dietary patterns, such as the Mediterranean diet. Its success depends on:

1. Nutritional literacy

2. Access to fortified foods or supplements

3. Consistent, varied intake of whole plant foods

4. A poorly planned vegan diet can be worse than an omnivorous diet if it relies heavily on processed, carbohydrate-rich foods, lacks protein diversity, or neglects micronutrients.

Ultimately, veganism is both a health choice and a lifestyle choice. Its benefits are clear, but so are its responsibilities.

References

1. Satija, A., & Hu, F. B. (2018). Plant-based diets and cardiovascular health. Trends in Cardiovascular Medicine.

2. Dinu, M., et al. (2017). Vegetarian, vegan diets and cardiovascular risk: A systematic review and meta-analysis. Critical Reviews in Food Science and Nutrition.

3. 3, Barnard, N. D., et al. (2009). A low-fat vegan diet improves glycemic control in type 2 diabetes. American Journal of Clinical Nutrition.

4. Appleby, P. N., et al. (2007). Comparative fracture risk in vegetarians and vegans. EPIC-Oxford Study.

5. Tong, T. Y. N., et al. (2022). Vegetarian and vegan diets and cancer risk. BMC Medicine.

6. Alvaro, E. et al. (2020). Plant-based diets and the gut microbiome. Nutrients.

7. Bloomberg Intelligence. (2021). Plant-Based Foods Market Report.

8. https://pmc.ncbi.nlm.nih.gov/articles/PMC10027313/

 

Understanding the Role of Medicines in Chronic and Emergency Care

Why Emergency Drugs Save Lives but May Not Cure Chronic Illness

 

Dear Bibi,

 

Thank you very much for your email and for your concern about your mother’s health.

Let me briefly share with you the background of our modern drug-based medical system. Much of it can be traced back to the influence of John D. Rockefeller. Interestingly, he himself used the natural healing powers of his own body to recover from severe illness, yet he later promoted petroleum-derived chemicals as “medicines” to the medical profession, naturally for commercial reasons. This is the beginning of what we now call allopathic medicine, the system that relies heavily on pharmaceutical drugs.

You may read the full story here:

The Secret of the Body’s Own Inner Medicines and the Rockefeller Transformation

https://scientificlogic.blogspot.com/search?q=rockefeller

Now, I want to emphasize something important: drugs are not useless. Many modern medications are truly lifesaving when used appropriately — especially in emergencies such as heart attacks, severe asthma, infections, trauma, anaphylaxis, or acute organ failure. In these situations, drugs and medical interventions can mean the difference between life and death.

Here are some of my articles explaining the vital role of emergency medicines:

https://scientificlogic.blogspot.com/search?q=emergency+medicine

https://scientificlogic.blogspot.com/search?q=Emergency+drugs

https://scientificlogic.blogspot.com/2025/08/emergency-protocol-for-management-of.html

 

However, problems arise when we begin using these chemical agents long-term to manage chronic lifestyle-related diseases. In such cases, medication often suppresses symptoms without addressing the root causes. Symptoms are not enemies ,  they are the body’s distress signals, asking us to intervene at a deeper level.

 

This is why many chronic diseases do not resolve. Instead, patients accumulate more symptoms, more diagnoses, and more drugs — a situation known as polypharmacy, which sadly becomes a major cause of complications and even mortality in the elderly. Controlling disease is not the same as curing it.

 

Fortunately, there is now an emerging and evidence-based discipline called Lifestyle Medicine, which is increasingly taught in medical schools internationally. It focuses on reversing chronic diseases by addressing diet, physical activity, sleep, stress, social connection, environment, and other root causes. Many countries — including Malaysia and Singapore — are now integrating lifestyle medicine and other traditional systems with allopathic medicine, just as recommended by the WHO.

No single healing tradition has all the answers. Modern medicine is sometimes like Dr. Jekyll and Mr. Hyde: one face offers lifesaving help, while the other face can unintentionally cause harm when used without balance. What we need is integrative healthcare — taking the best from each system to give patients real healing, not merely lifelong disease management.

I have written many articles on this subject, and I am happy to share them if they may help you or your mother.

Thank you again for writing, and I wish your mother comfort, healing, and guidance toward the best path for her health.

Warm regards,

Lim Ju Boo

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