These Thy Atoms


Thorough Materialism

The Catholic should be the most thorough materialist.” —Fr. Stanley L. Jaki[1]

True to the late Fr. Jaki’s dictum, I am a thorough materialist. I see nature as a system of interacting matter and forces. My four-year-old son has apparently acquired my enthusiasm. He heard me say that everything is made of atoms, and he took that idea seriously and pervasively. “Mom, are trees atoms? Mom, is my arm atoms? Wait. Am I eating atoms?” Those questions were soon followed with, “Move! I have to pee atoms!” To my knowledge, there is no historical record of the young Leucippus or Democritus asking such questions of their mothers in ancient Greece, but it seems reasonable to assume they may have pondered the implications of particles in their daily lives too. It is only natural that we inquire about the elemental inputs (and outputs) of our physical existence.

Of course, Fr. Jaki did not mean that we should only be materialists. He meant we should be “thorough” in that we ought to strive to understand all scientific discoveries and appreciate the disciplined study of the physical realm, for it is the study of the Handiwork of God. He wrote that line in a booklet titled Intelligent Design? His point was that intelligent design is an all-or-none proposition. Either we accept that the Creator is the consistently operating ground of all existence, or we do not. There is no half way, no saying: “Well, these genes sure seem intelligently designed. But those rocks? That dirt? No, those things are not intelligently designed.” Creation cannot be partially designed, and for that reason we should “thoroughly” explore science.

Nothing, in my opinion, makes that point more particularly than the atom. The atom is considered the fundamental particle of the elements from which the substances all around us are made, yet it is not the most elementary particle because the atom is made up of yet smaller entities. The atom is central in science. If atoms are designed, then everything physical is designed. Quantum physics builds up our models of atomic structure, and biochemistry grows forth from them. Atoms are the building blocks of physical materials, and any chemist will confirm that atoms themselves pose many a mystery to the human mind.

I am a Catholic convert, but I was a chemist before I was a Catholic. At first people assumed I had some insight into reconciling faith and science since surely I must have overcome one worldview to get to the other, trading science for faith where I once traded faith for science. But my views are not a “reconciliation” in the sense that I compromised either passion. My conversion did not involve picking sides. It was a “both/and” assent to a fuller view of reality. In time, I was excited to learn of the fruitful dialogue between scientists and theologians in scholarly spheres, but I was also frustrated. The media rarely covers the intense and brilliant discussions happening at the intersections of faith and science. The general public is instead treated to debates waged by people who are at the extremes of either atheistic or religious fundamentalism. Those opponents read nefariousness into the other side and debate their perceptions of each other. Public opinion, meanwhile, gets muddled in drawn out debates on the wrong questions until the faithful are left hesitant to trust either side. The religious debaters make it seem like the scientist debaters are trying to deceive the public, and the scientist debaters make it seem like only atheists can be scientists.

So I want to share my perspective about — my utter fascination with — this little fundamental, central, mystical thing we call the atom because I think it brings us all back to basics. I know what it is like to conduct scientific research while ignoring God, and I know what it is like to take the leap to see science from the higher vantage of philosophy and theology in, as I like to say, the “light of faith.” Thorough materialism, as it were, led me to God, and I am a more passionate materialist than ever before because I am passionate about Creation. Come, let us talk atoms.

The Particle at the Intersection

If we could dwarf ourselves down to the atomic realm, we would see a different set of physical laws than we are accustomed to seeing. A diamond is solid carbon. Carbon has an atomic mass of 12.01 grams per mole. A 1 carat diamond is 0.200 grams, so there are about 1.00 x 1022 atoms of carbon in a 1 carat diamond. Earth’s population is about 7,000,000,000 people, so if we could gather all the people in the world together into a 1 carat diamond and if those people were the mass of a carbon atom, there would be over 1.4 trillion Earth populations in that diamond. Crazy, huh?

The word “particle” really fails to explain the atom, however. Except in certain models like kinetic theory where it makes sense to think of atoms as hard spherical particles, the atom is better understood as a complex intersection between the physical and the non-physical realm. It is thought that atoms are mostly empty space with electrons described in mathematically probable orbits whizzing around unimaginably dense nuclei where gluons carry the strong nuclear force to hold quarks together as protons and neutrons. This strong force is actually better thought of as an interaction because without a relation to a particle it would not exist. (For an interesting Trinitarian theology comparison, see ST.I.40.)

The strong force is on the order of 1039 times stronger than gravity at the distance between protons,[2] which are measured to be 1.67 x 10-24 grams, very nearly but not exactly the mass of the neutron. But even as one speaks such large and small numbers, one cannot actually grasp their meaning. Neither can one really mentally picture the strong force. As strong as it is, the strong force does not extend outside of the nucleus. From there, the electromagnetic force, which is carried by photons (light), takes over and is itself many times stronger than gravity. The electromagnetic interaction is more easily grasp by the imagination, a physical interaction between electrically charged protons and electrons, the interaction governing the processes in chemical reactions so familiar to chemists.

If these details were not perplexing enough, the beauty of the periodic table ought to make one lay down and weep for joy. The periodic table was discovered not invented. One may need a PhD in Chemistry or Physics to navigate the beautiful equations in quantum mechanics that approximate our knowledge of atoms, but the discoveries of quantum mechanics and of the atomic realm manifest themselves right on the periodic table introduced to elementary students. What am I talking about with all this weeping and beauty stuff? Order. There is profound order, not just in the atom but among the atoms in relation to each other. Every element in the universe, including all those atoms of elements combined into molecules making up your environment, your body, your clothes, your food, and your air, is ordered, one by one, as if given marching orders, by an increasing number of protons in the nucleus. That is what identifies the elements — the number of protons — and there are no missing spots. Oxygen, and oxygen alone, has 8 protons. Carbon, and no other, has 6. Platinum has 78 protons, gold has 79, and mercury has 80. The protons in turn influence the number of electrons, whose arrangements seem to direct all chemical reactions, the arrangement that sends us wavelengths of light, each element having its own unique fingerprint. Chemical reactions happen or do not happen because of the relationship between electrons and protons. One has but to marvel at the periodic table to see that a wise and intelligent God “hast ordered all things in measure, and number, and weight.” (Wisdom 21:11)

Furthermore, every atom in our bodies came from the Earth whose matter came from supernovas whose matter came from, as far as we can tell, the earliest moments after the Big Bang. Every particle that composes our bodies at this moment has a unique history. Christians sometimes are hesitant to say that living things evolved from atoms, but why stop at atoms? We could say that our bodies evolved from the very beginning of time. It is mind-blowing indeed to consider what journey the atoms in our bodies might have traversed in the last 4.5 billion years on Earth or through the universe in the last 13.8 billion years. Did you ever wonder how many other bodies the atoms in a single body have occupied?

Just take a deep breath and contemplate this fact: You will never, ever know where the atoms you just breathed in have been in the universe. Now exhale. You just set a population of atoms free to continue their journey. Even the atoms in all the molecules on the end of your nose may have occupied some famous person’s body or some baboon’s behind or floated in some far away river. They may have soared in the Earth’s atmosphere, and they once existed in the vast reaches of the cosmos. The Anthropic Principle aside, your physical existence depends, moment by moment, on particles following exact laws of order that the best scientists today still cannot fully describe, which brings us to another fundamental profundity.

The atom is proof of the incompleteness of scientific understanding. Chemistry students in high school learn about the history of the atom from the conception of Democritus in ancient Greece to more than 2,000 years later when John Dalton formulated his atomic theory that all elements are composed of tiny indivisible particles that combine in simple whole number ratios to form compounds. The search for more fundamental particles continued into the nineteenth and twentieth centuries with the discovery of electrons by J.J. Thomson in 1897 and Robert A. Millikan, who calculated the mass and charge of electrons in 1916, and the nucleus and protons by Ernest Rutherford in 1911. Students learn about Niels Bohr in 1913 and his new atomic model which visualized the atom as a dense nucleus with a positive charge and a cloud of electrons at fixed energies called energy levels. They are taught that theoretical calculations and experiments led to a new model of the atom whereby an equation solved by Erwin Schrödinger describes the behavior of an electron.[3]

The over-arching story is that once firmly held ideas are frequently, if talking decades, overturned by new ones. Einstein thought the universe was static. Mendeleev once calculated the atomic weight of the ether, and Lord Kelvin thought atoms were vortexes in that medium. Thomson thought electrons were corpuscles, negatively charged particles surrounded by a soup of positive charge like raisins in pudding. Bohr thought the wave function represented the limits of what can be known about a physical system.

Today elementary particle research zig-zags ahead. In March 2014, astronomers thought they had detected the first evidence of primordial gravitational waves from 13.8 billion years ago with the BICEP2 telescope at the South Pole. There was much excitement because the detection of these waves had been predicted by Einstein as proof of the cosmic inflation that followed the Big Bang. In January 2015, the journal Nature reported that the gravitational waves discovery was “now officially dead.” [4] As it turned out, what astronomers thought were gravitational waves of cosmic origin was Milky Way dust. But the search continues because that is the nature of scientific research. It is provisional. It is incomplete. As such, it is also vibrant.[5]

In the summer of 2015, physicists at CERN, the European Organization for Nuclear Research where the discovery of the Higgs boson was reported in 2012, confirmed evidence of the pentaquark, a subatomic particle made up of five quarks predicted to provide further information about how stars form.[6] New research is so exciting that there are a reported 30,000 accelerators in operation around the world for discovery into particle physics. The United State Department of Energy Office of Science’s Stanford Linear Accelerator Center (SLAC) runs under Interstate 280 in northern California. The Large Hadron Collider runs underneath villages in the Swiss-French countryside, and the Cornell Electron Storage Ring, CESR, runs beneath the soccer, football and lacrosse fields at Cornell.[7] Who knows what stories will introduce the atom to students 100 years from now…

…and that is precisely why I want to tell you about my journey. If science is going to progress, I submit that future scientists must be scientists of faith. Hear me out.

Facing the Chasm

I was not religious when I worked as a chemist, and I know what it is like to conduct scientific research relying on order while not believing in God. I suspect agnostics, atheists, and all those otherwise called “Nones” find fulfillment in science because they are searching for truth and the exact sciences offers some mystery and truth. For me, the search fulfilled itself in the form of nanochemistry. Certain I was going to help save the planet, I joined a research team to help develop new nanometer-scale composite materials to artificially simulate the electron transfer process in photosynthesis to begin to develop new energy sources.

They were intelligently designed for sure. We layered photoreactive polymers on silica particles that were so fine a gram provided 150 square meters of surface area. Our sun was the second harmonic from a Spectra Physics Quanta Ray Nd: YAG LASER that produced 532 nm light aimed at a pinky-sized quartz cuvette of our designs. We were merely trying to simulate a single excitation and “jump” of an electron from one polymer to the other to maintain a brief charge separated state. The photons of light excited the electrons, and about 30% of the excited electrons transferred to another polymer, staying there for a charge-separated half-life of 21 microseconds.[8] We had enough success to publish in the Journal of the American Chemical Society, Coordination Chemistry Reviews, and a few specialized textbooks on the subject, but those successes only made the reality more awkward.

You see, heathen though I was, I knew that what we observed in all the mindless machinations of nature and what we can do in a super-sophisticated state-of-the-art university research lab is separated by, what I can only call, a chasm.

Each step of the electron transport chain in natural photosynthesis approaches near unit quantum efficiency, and the chain passes the electrons onward to do more work. Globally plants consume about six times more energy than the human race each year, silently giving off oxygen we need to breathe and glucose we need to live.[9] In spite of all I thought I accomplished, in the end I confirmed what the prologue of the Voet and Voet college-level Biochemistry textbook declares. “In all cases, our knowledge, extensive as it is, is dwarfed by our ignorance.”[10]

I used to marvel at trees with childlike awe and wonder, but that artificial photosynthesis project squelched it. Staring at a single leaf was like staring across a chasm I knew I could never cross. I knew too much about atoms and what they do in biological molecular machinery. I knew how exacting and rigorous the processes are, both within the atom and without it. I knew how efficiently photosynthesis chugs along, and I knew that photosynthesis is but a cycle in a much larger global cycle. And I knew my fancy experiments would never, ever come close to any of that.

It is still hard for me to look at a single leaf because I, likewise, know I could never fully appreciate the marvels clicking away before my eyes. Even if I could have simulated a part of the process exactly the way nature does it, I could never make time stop so I could analyze all that passes my failing human eyes in any second. We marvel over the beauty in snapshots of single snowflakes, but untold trillions of such masterpieces form in every snowstorm, fall to the Earth, and melt unnoticed. It as if the beauty of nature is mostly wasted on the blindness of humanity.

Laughably, we nanocomposite artificial photosynthesis groupies were but puny observers and manipulators of laws magnificently beyond the work of human hands, and we knew it. Everything we did was a manipulation of matter obeying laws that came from…Somewhere Else. You do not often hear people who lack a belief in God talk about how it feels to grapple with science. Let me tell you. When you rob yourself of the ability to see beyond science, science becomes just as dead as it becomes mechanical. “Perhaps,” I remember thinking, “this is what they mean when they say the meek inherit the Earth.” To see the beauty of the world, you need docility not arrogance.

How did I deal with the denial? I tried to tell myself it did not matter. When we use mobile phones, we do not feel angst if we do not know how they work. We do not need the answer, and the answer would not demand much of us in return. With similar nonchalance, I simply shelved those bigger questions because I did not need the answers to do my work. It was only when I wanted to pursue a life of faith that I had to face up to that chasm I ignored. No one thinks mobile phones are the key to salvation (let us hope), but you need courage to face the supernatural reality about everlasting life. Once you leap into that unknown, you do not know what the truth will demand of you. You do not know if you will fall to your death or find some way to fly.

Every day I worked as a chemist, I knew I stood on a precipice with my back to that expanse of truth I was not willing to see. At times, it was hard to convince myself not to care. I worked, you could say, by looking down at the ground so I could keep my feet safely planted there, chiseling grains off the crag I clung to. I did not dare look up or out even though the scientist in me, deep down in those quiet moments when I let my mind wander, wanted to know the big truth beyond me. The poet, Francis Thompson, said faith pursues you like the Hound of Heaven, a grace that takes no leave, not in the “nights” or “down the days,” the “arches of the years” or the “labyrinthine ways,”[11] but for me faith was more like the elephant in the laboratory. It was obvious and enormous, and ultimately impossible to ignore. A scientist who does not believe in Creation has to daily ignore the elephantine fact that she does not even know why the truths she strives to discover are there. She has no fundamental explanation for why she cares about atoms. She cannot answer the ultimate “Why?” a question most dear to her scientific heart.

People hold scientists in high regard as intellectuals, but conducting scientific research does not instill in a person broad knowledge traditionally associated with intellectuals. The work is often like grunt work. The intellectual aspect takes a scientist from broadly absorbing scientific literature in a specific area of research into narrower and narrower, exceedingly specialized scientific method cycles to hypothesize and test exceedingly specific questions. I guess if you wanted to plot it, a scientist’s knowledge looks like a vertical spike. Arguably, this spiking of the intellect was my source of angst. Scientists need to know more than science, or they cannot understand science as science.

As it turns out, granting assent to the truths of faith was the most intellectually satisfying leap I ever dared to take as a scientist and more importantly as a person. When science is informed by faith and faith is informed by science, it is like looking out an airplane window on a clear day. You can see the details of the land you live and work on, where you thoroughly know the grains and crags, the contours and machinations, and you can also see how that land fits in with a bigger multi-dimensional world. To see science in the light of faith is, simply, to see more of reality. And science must be about reality.

Three Simple Returns

So I propose three returns, for anyone interested in the faith and science dialogue, be you children, high school students, university students, young professionals, parents, educators, seminarians, priests, or all those brilliant scholars participating in the faith and science dialogue: 1) Return to first principles. 2) Return to an insistence on the limits of science. 3) Return to childlike awe and wonder in everyday things.

The first principles are in the Creed. “I believe in God the Father Almighty, Creator of Heaven and Earth.” Great care should be taken to never give the impression that science somehow shores up faith. If we ever give the impression that we need to sell faith with science, we send the message that maybe we think faith is not reasonable after all. Scholars know science cannot prove or disprove God, but there is an appeal in popular culture to invoke science as providing evidence for faith, for example in the case of the Big Bang.

While scholars cite the Big Bang as evidence there was a beginning in time, they know they are citing it as inductive proof, that is, as proof that corroborates a larger conclusion but does not demand its own conclusion. Deductive reasoning goes the other way. The deductive reasoning of metaphysics can lead to only one conclusion that there had to be a beginning in time and a Creator, and this sound reasoning ought to guide scientific insights for it is a waste of time for a scientist to pursue metaphysical absurdities.

For example, such is argued in Fr. Robert J. Spitzer’s 2010 book, New Proofs for the Existence of God: Contributions of Contemporary Physics and Philosophy.[12] The title may be misleading if not read carefully. Fr. Spitzer does not argue that science proves the existence of God, but he argues that contemporary physics points to the same conclusion that metaphysical deductive reasoning discovers — that the one Unconditioned Reality is the continuous Creator of all else that is. In doing so, Fr. Spitzer shows how sound philosophical reasoning might lead scientific questioning. His book offers the kind of guidance a scientist not trained in philosophy needs.

Nevertheless, the public needs to hear this advice before they ever get to such a book about proofs of God: Whether physics in our lifetime points to a beginning or not, we still affirm a beginning because we hold that truth in faith. Before the Big Bang theory when some thought the universe was infinite, the Church did not change her Creed, nor will She in the future if scientists include the assumption of infinite time in their equations.

Therefore, and secondly, scholars must make absolutely clear the limits of science. Fr. Jaki was adamant about this distinction. Physical and biological sciences are limited to physical and biological questions. To physics, all objects including living things are systems of particles. Living objects differ from non-living objects in their degree of complexity. Biology is only a spectator of life. Biology observes, describes, and sorts life’s characteristics once the fiat of life has begun. Metaphysics, philosophy, and theology are separate disciplines with their own methods. They deal with meaning, purpose, and destiny, and like science, they are uniquely human endeavors.

I never liked Stephen J. Gould’s NOMA (non-overlapping magisteria) theory. He held that science and theology were entirely separate spheres only touching borders at times as if they were children afraid of cooties. I think of it differently. Once lifted by faith, it was as if I could gaze down and see science among the other disciplines. I could see how they fit together because I had the higher perspective. We need to know about the atom, and we need to learn about math, language, philosophy, theology, history, and the arts. A classical education encourages this broadness. Bring back classical education.

Last, to rediscover the childlike awe and wonder we simply need to remind ourselves what we already know in the mundane details of daily life. For example, like many mothers, I cook up systems of atoms in my domestic laboratory and serve them to the living analytical machines I call my family. My son, whose antics are mentioned in the beginning of the essay, demonstrated this last point as only children can. A few days after his litany of questions probing the extent that atoms comprise the physical world, I served him a plate of spaghetti and meatballs, his favorite. Where a lesser materialist would say, “Bless us O Lord and these thy gifts,” he went one step more specific.

“Bless us O Lord and,” with a self-satisfied grin, “these thy atoms.”

That is how we should approach science in the light of faith. We should gratefully approach the scientific table in the light of faith as a form of worship to know and love God. Contrary to the conflict myth, science has united the global community into one big discussion about our future, and I am happy to announce that philosophers and theologians are indeed taking their rightful seats at that table to guide the way. Will you people of faith join them? Whether another person sees the atoms as gifts from God or whether the other person prays some other way, we should never set aside a confident faith in Christ and His Church, not before meals and not before science. We start with our prayer of thanks. We see the material realm for the beauty that it is, and our radiant faith illuminates the discourse about all those atoms.


This essay was a recipient of the Re-Engaging Science in Seminaries essay award.


Rev. Dr. Thierry Magnin
Catholic University
Lyon, France
Physicist, Priest, and Rector

Dr. Ignacio Silva
The Ian Ramsey Centre for Science and Religion
Oxford University, UK
Science-Theology Researcher and Program Coordinator

Professor Emerita Doris Donnelly
John Carroll University
Cleveland, OH
Theologian and Project Director of Re-Engaging Science in Seminary Formation

Funding for this initiative at
University Heights • Cleveland, Ohio
has been provided by the
John Templeton Foundation.

Stacy Trasancos is available for interviews.
Contact her at


[1] Stanley L. Jaki, Intelligent Design? (Port Huron, MI: Real View Books, 2005), p. 5.
[2] Constantinos G. Vayenas and Stamatios N.-A. Souentie, Gravity, Special Relativity, and the Strong Force: A Bohr-Einstein-de Broglie Model for the Formation of Hadrons (New York, NY: Springer, 2012), p. 25.
[3] Michael, Wysession, David Frank, Sophia Yancopoulos, Physical Science: Concepts in Action (Boston, MA: Pearson/Prentice Hall, 2006), chapter 4.
[4] Ron Cowen, “Telescope captures view of gravitational waves,” Nature Breaking News (2014).
[5] R. Aaij et al. “Observation of J=ψp Resonances Consistent with Pentaquark States in Λ0 b → J=ψK−p Decays,” Physics Review Letters, (14 August 2015), PRL 115, 072001.
[6] Since this essay was written, the story continues, “Einstein’s gravitational waves found at last,” Nature (16 January 2016).
[7] Sarah Witman, “Ten things you might not know about particle accelerators,” Symmetry Magazine (Department of Energy, April 15, 2014).
[8] Steven W. Keller, Stacy A. Johnson (Trasancos), Elaine S. Brigham, Edward H. Yonemoto, and T. E. Mallouk, “Photoinduced Charge Separation in Multilayer Thin Films Grown by Sequential Adsorption of Polyelectrolytes,” Journal of the American Chemical Society (1995), 117, pp. 12879-12880.
[9] “Renewable biological systems for unsustainable energy production,” FAO Agricultural Services Bulletins (1997).
[10] Donald Voet and Judith G. Voet, Biochemistry (New York, NY: John Wiley & Sons, 1990), p. 16.
[11] Francis Thompson, “The Hound of Heaven,” A Poem (1859-1907).
[12] Robert Spitzer, New Proofs for the Existence of God: Contributions of Contemporary Physics and Philosophy (Grand Rapids, MI: Wm. B. Eerdmans Publishing Co., 2010).

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About the Author

Stacy Trasancos is a wife and homeschooling mother of seven. She holds a PhD in Chemistry from Penn State University and a MA in Dogmatic Theology from Holy Apostles College and Seminary. She worked as a chemist for DuPont in the Lycra® and Teflon® businesses.

She teaches Chemistry and Physics for Kolbe Academy Online and Homeschool Program and serves as the Science Department Chair. She is teaching a set of summer mini-workshops titled "Science in the Light of Faith" for students, parents, other educators, or any Christian interested in the nuts and bolts of navigating science.

Similarly, she is teaching a "Reading Science in the Light of Faith" at Holy Apostles College & Seminary next Fall (2016). The course is funded by a John Templeton Foundation grant through John Carroll University for teaching science in seminaries. She is on the Board of Directors for ITEST (the Institute for the Theological Encounter with Science and Technology) where the essays from the course will be shared with the public.

Also in the Fall of 2016, she will teach a "Theological History of Science" course at Seton Hall University, where her mentor, the late Fr. Stanley L. Jaki was a distinguished professor. She is the author of Science Was Born of Christianity: The Teaching of Fr. Stanley L. Jaki.

Her new book, Particles of Faith: A Catholic Guide to Navigating Science is forthcoming with Ave Maria Press...

She teaches, researches, and writes from her family's 100-year old restored mountain lodge in the Adirondack mountains, where her husband and children (and two German Shepherds) remain her favorite priorities. Here is her website.

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  1. A few months ago, I was contemplating the scripture passage of Jesus healing the leper.
    The leper asked , if Jesus wished, he could heal him. Jesus said, I do wish it, and he was “immediately” made clean, which in the case of leperacy, may have included the replacement of lost body parts.
    Now my point is on the “age appropriate” action of a miracle.
    A miracle is termed ” an acceleration of creation”, thus the leper being made whole included age appropriate body parts to correspond to his age at the time.
    My point is, if the leper was 35, his new parts where age appropriate 35 year old parts.
    Now on to the Creation story.
    God claims to have made all of creation in 6 days. A mere reflection of a created thing “time” in itself, but a decree of a period none the less. My point is if Jesus, “through whom all things were made” created, out of nothing, new and age appropriate body parts for a leper, could He have not have done the same thing with creation, incuding in it a past?
    The old addage, “what was created first, the chicken or the egg”?
    My answer is both!
    God created time with a past, well ordered, proper and with evidence, just like the lepers body parts, with geological evidence of a past, starlight streaming to earth in its proper travel periods, etc.
    So we can beleive in evolution in that it is a properly ordered creation, but like the lepers skin, did not need to be created in the normal time frame of formation but in the super natural acceleration of a miracle.

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