Science in Everything Everywhere

Letter from the editor

Emily Danzinger

Political Science and International Studies, Class of 2025

Editor-in-Chief, UMiami Scientifica

Hi everyone!

I hope everyone's had a great Spring semester so far! I'm so incredibly excited to finally launch Issue 26: Science in Everything and Everywhere, All at Once. After our Issue 25 about psychology, I wanted to take one step further, going beyond standard realms of human perception regarding the world we observe and into a realm in which many claim science to be diametrically opposed to. We challenged our writers to think outside the box and examine how science ties in with things we may not usually expect it to, whether poetry, religion, or even metaphysics. I also encouraged our writers, specifically those enrolled in MIC 280, to find the parallels between our own bodies and the massive universe that surrounds us, just as a reminder of our creationary connection to the cosmos. I'm so proud of all the hard work that went into this issue, and all of our incredible staff members who have continued to make the magazine theirour - own. This issue carries with it the feeling of a continuing Scientifica renaissance, and I'm so glad it is finally yours. Have fun, stay curious, and don't stop trying to fit square cubes in round holes - one day, it might work. :)

Letter from the editoriaL advisor

"Ever have that feeling where you’re not sure if you’re awake or dreaming?" – Neo, The Matrix, 1999

Maybe we are living in a simulation or one of many universes (multiverse). How would ideas like this fit into our religious and scientific beliefs? What is consciousness without spirituality? So many questions, and can we really answer them? This issue will look at some of these but also, we will look at our physical world around us and how it relates to our bodies. Please enjoy this issue and reflect on your existence.

Roger I. Williams Jr., M.S. Ed. Director, Student Activities Advisor, Microbiology & Immunology Editorial Advisor, UMiami Scientifica

Emily Danzinger

Ethan Bentley

Aarohi Talati

Veronica Richmond

Ethan Tieu

Vrinda Gupta

Shirley Pandya

Yewande Shitta-Bey

Luke Sims

Francesca Dostillio

Michel Huyghe

EDITOR IN CHIEF

MANAGING EDITOR

COPY CHIEF

ART & DESIGN DIRECTOR

DIRECTOR OF WRITING & CREATIVE WRITING

DIRECTOR OF PUBLIC RELATIONS

DIRECTOR OF PHOTOGRAPHY

DIRECTOR OF DISTRIBUTION

DIRECTOR OF FINANCE AND ADVERTISING

CO-DIRECTOR OF COMMUNITY OUTREACH

CO-DIRECTOR OF COMMUNITY OUTREACH

SCIENTIFICASTAFF2024

Board of advisors

Barbara Colonna Ph.D.

Senior Lecturer

Organic Chemistry

Department of Chemistry

Richard J. Cote, M.D., FRCPath, FCAP

Professor & Joseph R. Coutler Jr. Chair

Department of Pathology

Professor, Dept. of Biochemistry & Molecular Biology

Chief of Pathology, Jackson Memorial Hospital

Director, Dr. Jonn T. Macdonald Foundation

Biochemical Nanotechnology Institute

University of Miami Miller School of Medicine

Michael S. Gaines, Ph.D.

Assistant Provost Undergraduate Research and Community Outreach

Professor of Biology

Mathias G. Lichtenheld, M.D.

Associate Professor of Microbiology & Immunology

FBS 3 Coordinator

University of Miami Miller School of Medicine

Charles Mallery, Ph.D.

Associate Professor

Biology & Cellular and Molecular Biology

Associate Dean

April Mann

Director of the Writing Center

Catherine Newell, Ph.D.

Associate Professor of Religion

Leticia Oropesa, D.A.

Coordinator Department of Mathematics

*Eckhard R. Podack, M.D., Ph.D.

Professor & Chair

Department of Microbiology & Immunology

University of Miami Miller School of Medicine

Adina Sanchez-Garcia

Associate Director of English Composition

Senior Lecturer

Geoff Sutcliffe, Ph.D.

Professor of Computer Science

Yunqiu (Daniel) Wang, Ph.D.

Senior Lecturer

Department of Biology

*Deceased

seCtIon edItors

Universe R Us: Aarohi

Research:

Veronica

Writers

a guide to Just Being a roCk

The Idea of Infinite Universes

Infinite Worlds Theory

This never-ending gum expansion is the story behind the Infinite Worlds theory, one of the explanations behind your possible alternative rock-persona. This theory believes that our universe is not the end, but just the beginning. It basically says that if you were to fly to the “end” of our universe, you would just go into another universe and another, infinitely. This theory says that our Earth is not the only one, but it repeats due to the infinite nature of space combined with the composition of matter. Unfortunately, there is no way to prove this theory because these Earths are always expanding, getting further and further away from us. So, lucky for you, you won’t have to worry about another version of you traveling across the multiverse to meet you, unless they figure out a way to travel at the speed of light and live for billions of years so that they can reach you.

By: Madyson Carter | Design: Dominique Thomas

Are you looking to escape reality? Are you stressed with finals and other trivial human worries? Would you like for just one moment to be free of everything? For the small price of inventing a way to travel the multiverse, you can “just be a rock”. That’s right, there’s actually a universe where you are just a rock, or a bird, or a movie star, or anything else you can think of. In fact, there’s a version of you reading this article, maybe sitting in another room, or in another country, or in another universe. These versions of you are likely existing right now, but how they are existing is still up for debate.

One thing generally agreed on amongst scientists is how the multiverse started, with a Big Bang. Our universe started from a single, tiny, hotspot that eventually exploded. This explosion expanded at light speed for fractions of a second, to create our universe. This brief expansion is referred to as cosmic inflation, which stretches and smoothes space at light speed. That seems complicated, but imagine space as a piece of gum. Now imagine this small piece of hot gum suddenly expanding at such a fast rate you cannot even see it move. Before you could even recognize that this stretching occurred, silence. The gum is suddenly an infinitely long and large area that is abruptly still. This sticky situation gets complicated when you realize that the inflation may have stopped in our universe, but other universes are still experiencing it. This stretching of gum is occurring in some areas, but not in others, thus separating the inflating universes from the stationary ones. Should you find that absurd, it doesn’t stop there. The stretching universes are creating even more inflating universes, which creates more universes, and more, and more, and more, and… well you get the picture. Now, does it still seem crazy that you are a rock in one of them?

Many Worlds Theory

If you do want to meet this alternate version of you, there’s still hope; all you have to do is change the rules of quantum mechanics so quantum objects can travel between worlds. Easy task, right? This solution is related to the other theory behind the multiverse: the Many-Worlds theory. Unlike the Infinite Universe theory, this theory is much more supported due to experiments in quantum mechanics. The Many-Worlds theory at its core says that our universe is branched into many parallel universes that are constantly branching off of each other, but never bumping into each other. This theory is thought to be almost 95% true, based on the assumption that quantum waves are always evolving and are in every physical reality. Basically, the Many-Worlds theory is thought to be true based on the theory that every action leads to countless outcomes. You can try this out now. Grab a piece of lined paper and a pencil, now quickly poke a hole randomly through the paper. You just created parallel universes. Let’s say the hole you created is perfectly centered in the middle of the paper. There are now infinite universes where the hole is slightly to the right, or at the top, or through the 22nd line, or any other possible places on the paper. Congratulations, you are now the parent of an infinite amount of universes!

Just A Rock

Now that you’ve dove deep into quantum mechanics, astrophysics, and all these other difficult subjects, I have a surprise: it’s all just a theory. Yes, unfortunately, you read that right. After all this research and experimentation, these are just theories at the end of the day, and likely will always remain that way. This just emphasizes how unknown the universe is and how small we really are in the grand scheme of the infinitely expanding multiverse. As Evelyn said in Everything, Everywhere, All At Once, “every new discovery is just a reminder –we’re all small and stupid.” I hope this encourages you to marvel at the complexities of our personal universe, no matter how complicated it may seem compared to a world where you can just be a rock.

The Hidden World

by: Ethan Bentley

Illustration & Design: Vrinda Gupta

The Science of Dark Matter and Dark Energy

As a species, humans have made incredible advancements. We have evolved from learning to make the first tools in antiquity to attempting to grasp the wonders of the natural world. At times, it can seem like the only real frontiers of science lie far out at the edge of the galaxy, or deep at the bottom of oceans. Yet, sometimes, the universe likes to remind us just how little we understand.

In 1933, Fritz Zwicky, a Swiss astronomer, was studying at the Mount Wilson Observatory in California, gazing at the Coma cluster of galaxies. It was then that he discovered that the mass of all of the stars was only capable of roughly 1% of the gravitational force necessary to keep the galaxies within the cluster from pulling away. To account for this anomaly, Zwicky proposed the existence of an unobservable form of matter that would cause the gravitational pull; he called it dark matter. Despite this initial theory, the concept of dark matter would not be truly accepted until the 1970s, when Vera Rubin and W. Kent Ford confirmed that the presence of dark matter was necessary to keep galaxies from flying apart. In a typical galaxy, normal mass only accounted for 10% of the mass needed to keep stars orbiting the center of their galaxy. Through the years, the presence of dark matter has been

reaffirmed due to its gravitational effects. Not only do we know that dark matter exists, but we know that there is significantly more dark matter in the universe than there is normal matter. More striking is that we can even view it in a sense. Due to dark matter’s lack of interaction with light, there are places in the universe where light bends around locations with a high concentration of dark matter. The exploration into the field of dark matter reveals how little we know about our universe: we have shown there to be a form of matter that is, for all intents and purposes, invisible, yet it is shown to be far more abundant. Further highlighting the mystery of our reality is the proposed idea that not only does dark matter exist, but so does a substance known as dark energy. Much like dark matter, dark energy does not interact with light and is also currently impossible to measure, but its existence is shown through the effect it has on the universe. In 1929, Edwin Hubble experienced the phenomenon of redshift, where the wavelength of light emitted by galaxies shifted to red on the electromagnetic spectrum and became fainter as it appeared further from Earth. This led Hubble to conclude that the universe is expanding based on the idea that as galaxies move further away, their wavelengths stretch, causing them to experience a greater degree of redshift. In 1998, astronomers found that not only is the universe expanding, but this expansion is accelerating,

which has been attributed to the presence of dark energy. Dark energy is viewed as a repulsive force that, while not well understood, is responsible for driving the universe apart. The idea that there is a force in contrast to gravity, driving the universe apart, was first theorized by Einstein in what is known as his “cosmological constant”. While Einstein viewed the addition of the constant as a blunder, evidence for this has come in the form of dark energy, which is seen as an increasing substance that is expanding the universe. Much like dark matter, the presence of dark energy is used to further explain the deficit of the impossibly low amount of mass in the universe. Accounting for these proposed theories, our universe is composed of approximately 68% dark energy, 27% dark matter, and leaving us with just 5% of everything we see to be normal matter. This determination forces us to wonder how much we know about our world, seeing as we can only view

5% of the entire universe, suggesting that we only experience a tiny portion of reality. To complicate matters, we have not been able to determine what dark matter and dark energy are. Currently, there are many efforts to find particles of dark matter or dark energy, but none have been successful. While this may be confusing to the average person, it serves as a stark reminder that humans still are just touching the surface when it comes to understanding the makeup of our universe. These theories may feel abstract and irrelevant to our daily lives because we cannot see or understand their importance, but it is essential to understand why we seek to uncover these mysteries. Discovering the dark parts of our universe will allow us to gain a better understanding of physics as a whole, which could lead to significant scientific and technological innovation. As scientists search for answers in the hidden world of dark matter and dark energy, it is important to understand that the frontiers of discovery can be found all around and there’s no telling what the next mystery will reveal.

Two Pumps of Global Warming

How Rising Temperatures Have "Bean" Affecting Your Coffee

by Ethan Tieu Illustration & Design: Veronica Richmond

In the realm of bustling college life, coffee reigns supreme as the unofficial elixir of alertness, a trusted companion through early morning classes and late-night “study sessions.” In fact, we ‘Canes love coffee so much that we’ve somehow coerced Starbucks and Peet’s into coexisting on the same campus. But despite our universal addiction, have you ever asked where your brew comes from? Have you ever considered what variety of coffee you drink? Or has the thought of climate change (yes, that climate change) wiping your go-to blend from the Earth ever crossed your mind? In this coffee-fueled ramble, I will walk you through how the coffee industry is changing under the pressure of climate change and why efforts to save our favorite blends may be misplaced.

Today, one coffee variety alone accounts for about 60% of global production: arabica. Celebrated for its delicate flavor and aromatic qualities, arabica is the foundation of many coffee chains. In fact, both Starbucks and Peet’s exclusively use arabica beans in their blends. However, our favorite caffeine champion has one significant vulnerability that accounts for much of the unease in the present-day coffee industry: its sensitivity to temperature fluctuations. As global warming drives temperatures higher, arabica coffee faces a dire threat. Studies reveal that these rising temperatures are detrimental to arabica

production not only by decreasing the quality of arabica beans, but also by drastically decreasing production. In fact, academic research has predicted that global warming will reduce the areas suitable for arabica farming by as much as 66% by 2041–2060. With the coffee industry almost solely relying on arabica, your favorite blends may taste much different, or even disappear, in 20 years’ time.

But fret not! There are numerous solutions that will likely prevent such a disaster from happening. Let me introduce one of these key players: robusta. With arabica under attack, robusta coffee emerges as an alternative with distinct advantages. robusta, known for its more robust, bitter taste compared to the milder arabica and its status as the second most popular coffee variety, has two unique features: 1) it has nearly twice the caffeine of arabica and 2) it is naturally resilient to high temperatures. This agricultural robustness (last robusta pun, I promise) offers a potential solution to the challenges posed by global warming. By giving robusta a shot (sorry, I lied) and incorporating it into our coffee blends, we may be able to fortify many of our beloved brews against rising temperatures. While many have criticized this circulating idea due to the distinct taste of robusta beans, here’s a hot take from an avid black coffee enthusiast who has tried robusta: with its stronger taste and higher caffeine levels than arabica, robusta may be what many are looking for in their morning cup of joe.

As opposed to accepting robusta beans into their fold, Starbucks has implemented a unique solution to protect their arabica brews from rising temperatures. For more than ten years, Starbucks has been investing in research to breed new varieties of coffee trees that are more productive and resilient. Earlier this year, Starbucks announced that it had successfully produced six new arabica varietals that not only taste as good as conventional arabica varietals, but are also more resistant to rising temperatures. With the resilience of varieties like robusta and Liberica but the flavor of arabica, these novel varieties seem like the best of both worlds! With these efforts, Starbucks aims to keep its coveted arabica blends in stock even in the face of global warming — undoubtedly great news for coffee lovers everywhere.

But what will happen if temperatures continue to rise? Will greater proportions of temperature-resistant varieties continue to be added to arabica blends? Will Starbucks, or maybe even Peet’s, continue to develop newer climate-resistant arabica varietals? These two solutions, while certainly having momentum, highlight a key oversight of many approaches: we often fixate on implementing solutions that are “upstream” from the source of the issue. Mixing different varieties may fortify our favorite blends, but the extent of this mixing will only become more drastic as long as arabica trees continue to produce lower yields. Creating more resilient arabica varietals may provide for greater yields, but new, more resistant varietals will have to be created for as long as temperatures continue to rise. Therefore, if we are to fight for our coffee in a way that provides enduring support, the best way to do this is by attacking the root of the issue: climate change.

You’ve all heard about climate change a million times, but now a new asset is at stake: your coffee — the same coffee that has gotten you through your earliest mornings, latest nights, and midday narcoleptic episodes. As coffee lovers and responsible consumers, we must weigh in on the future of our invaluable companion. While companies may continue to mix new varieties and develop new trees, it is largely up to us to make responsible, environmentally conscious decisions. And yes, I know this may sound a teeny bit anticlimactic, and yes, I know that you’ve been told a thousand ways how to do this. But the next time that you’re holed up in the stacks cramming for finals with a trusty cup of Peet’s by your side, consider that for all your coffee has done for you, turning off your dorm lights when you step out is the least that you can do.

In the Beginning: Bridging Science and Genesis

by Michel Hughye

& Design: Caitlin Torralba

“In the beginning , G o d detaerc eht snevaeH dna t h e Earth. ”

Whether it was your parents, your Sunday school teacher, or Veggietales, at some point or another, almost everyone has at least heard of the Genesis account of creation. It not only serves as the introduction to the Bible, but in the eyes of Christians and Jews alike, the introduction to the universe itself. However, the Genesis account of creation has not been immune to being one of the most scrutinized passages in the debate between science and religion. So the question must be asked: Can the Genesis account coexist with science and logic?

Illustration

What is Genesis 1:1 saying?

Examining the very beginning in verse 1:1, we read those famous words, “In the beginning, God created the heavens and the earth.” When breaking down what this verse means, most of the words are simple enough to understand, but the one exception is the word “heavens”. What does it mean that God created the “heavens”? The book of Genesis was originally written in Hebrew, a language that oftentimes has words with multiple meanings in the context of 1400 CE Judaism, yet our modern translation of these words into English can often fail to capture these cultural meanings. The word “heavens” is one of those words. To the Hebrews of the time as seen throughout the rest of the Old Testament Scriptures, the “heavens” was a term used to describe the space above the earth, the firmament of the sky, the atmosphere surrounding the earth consisting of the sun, moon, and stars, and the overall universe as they understood it. Looking at the text through the lens of the original Hebrew context, it can be seen that Genesis 1:1 is referring to the creation of the universe.

In light of the massive claim of Genesis 1:1, the very first phrase of this verse can often be overlooked, yet it makes a miraculous claim of its own. Genesis 1:1 starts with the phrase “In the beginning”, which at first glance might appear as merely a modifier for the claim that follows. However, we must consider what is being said in the text, that when God created the heavens and the earth, it was the “beginning”. The beginning of what? The universe yes, but also time itself. Genesis 1:1 cements creation as not only the beginning of the universe but of time itself, stating that before the universe began, there was nothing, no time, no gravity, no laws of physics, nothing.

What about Science?

The initial assumption of Genesis 1:1 is that before this creation, there was nothing, which is consistent with how brilliant scientific minds have viewed the time before the universe. For example, take Stephen Hawking’s “no-boundary proposal”, which states that the universe over time is like a cone, with a radius of zero at one end representing the beginning. As time moves since the beginning of the universe, the radius grows larger. The proposal essentially states that the universe started from a point of nothing. Hawking himself even said “Asking what came before the Big Bang is meaningless…because there is no notion of time available to refer to,” and “It would be like asking what lies south of the South Pole.” Thus, the claim of Genesis is not in disagreement with science that before the universe, there was indeed nothing. Now if we take a look at modern science’s idea of the beginning of the universe, Genesis 1:1 doesn’t seem so absurd. The most generally accepted theory of the creation of the universe in the modern scientific community is the Big Bang Theory. Simply explained, the Big Bang Theory asserts that the universe began in a single instance, at a single point, that experienced an explosive expansion that resulted in the universe as we know it. Both the Genesis account and the Big Bang Theory assert that there was a point at which there was no universe, but at some definite moment, there was an event that created the universe.

nation? The belief that God created the universe is not one that can be proven outright. Nobody was there, nobody witnessed it directly, and in many ways it is indeed a matter of faith. However, when examining the creation of the universe in light of philosophical and logical ideas, there are genuine connections that can be made.

Thinking of the topic logically, we can take a trip back to the 5th century BC, when a Greek philosopher named Parmenides coined the phrase “Ex nihilo, nihil fit”, or in modern vernacular, “out of nothing, nothing comes.” This brief phrase encapsulates the idea that everything we know about the universe supports the idea that where something is created, it has to be created from something; things don’t just appear out of nowhere. When something exists, it exists because it was created by or from something else. It is this theory that we abide by every time we drive our car and don’t fear that a tree will spontaneously appear in the middle of the road and make us crash. Everything in this universe, including the universe itself, demands that something of an order greater than itself caused it to be.

Taking a step forward to the present, we can more closely examine what the cause of the universe logically may have been. At the core, there are two causal explanations for everything that occurs in the universe: scientific and personal. Dr. William Lane Craig, a renowned analytic philosopher and apologist, defines scientific explanations as “based on laws and initial conditions” and personal explanations as based on “an agent and his volitions”. Put simply, if you were to ask me why there was a popping sound coming from the microwave, a scientific explanation would be that the microwaves hitting the water molecules of the corn kernels are causing them to vibrate, generating heat, resulting in the kernels popping, whereas a personal explanation would be “I’m making popcorn.” When examining the first physical state of the universe, Dr. Craig makes the assumption that there can be no scientific explanation being that it is the first physical state, having no laws or initial conditions. As a result, this leaves a personal explanation to be the only logical explanation for the universe. As for this personal explanation, it must also be timeless, spaceless, and immaterial, again being that time, space, and matter were not present. Only two objects can meet this criteria, an abstract object, like a number or an equation, or an unembodied mind. However, abstract objects are just that, abstract. They do not have causal effects, leaving the remaining option to be an unembodied mind or person, one like the God to which Genesis 1:1 and the whole Bible points, a God who is personal, yet is Spirit (John 4:24) and operates outside of space and time (Isaiah 57:15; Psalm 90:4).

While the Genesis account is ultimately one to be taken by faith, as even the book of Hebrews in the Bible states “By faith we understand that the universe was created by the word of God, so that what is seen was not made out of things that are visible,” it can also be seen that it is by no means in contradiction with science and the Big Bang Theory, and even offers a potential explanation for what truly happened “in the beginning”.

Is God a Viable Explanation?

Even if Genesis and science are on a similar page of the event of the creation of the universe, is God a viable expla-

apop

finding meaning

By veRonicA RicHmond

illustRAtion & desiGn: veRonicA RicHmond

If you’ve ever looked up on a nice day, odds are good you’ve found all sorts of cool shapes in the clouds. As this is a relatively commonplace experience, you might not have given it a second thought. It turns out, though, that the root cause of these fluffy hallucinations has far-reaching, serious impacts.

connections are called apophanies. As opposed to epiphanies, where a true and insightful connection is discovered, an apophany is the false realization of meaning. In contexts like cloud patterns, this may seem harmless, but apophanies can have serious consequences. One of the most infamous products of apophenia is the gambler’s fallacy, wherein we believe that the probability of a future random event is impacted by the results of prior events. This often results in predicting the opposite of the previous outcome, especially if there has been a streak of the same result. For example, if you flip a fair coin five times and they’re all heads, you are much more likely to predict that the next one will be tails when, in reality, the odds are still 50%. In 1913, the financial impact of this fallacy famously came to a head at a casino in Monaco. When the last ten spins of a roulette wheel had landed on black, gamblers began to bet against black, as apophenia convinced them that red was overdue. However, the trend continued, and their belief that the next spin had to be red strengthened. As the wagers and crowds grew, so did their losses with each black spin. All in all, the ball didn’t land on red until after 26 backto-back blacks. The casino had hit the jackpot thanks to the gamblers’ misplaced faith in apophenia.

This same misguidance is often responsible for poor decisionmaking in the stock market, as investors place too much confidence

henia in the meaningLess

in trends and other random patterns. This form of apophenic data misinterpretation also plagues scientists in the form of Type 1 errors. These false positives arise from assigning importance to perceived patterns (such as clusters or sequences) that are not actually responsible for the observed result. Especially when under immense pressure to find and publish meaningful results, researchers will often inadvertently fall back on their apophenia and intently search for meaning in their results until they convince themselves that there is something significant there. In fact, when two professors from Dartmouth and the University of Maryland analyzed a random sample of articles from five of the top strategy journals, they estimated that at least 12%, but even as many as 40%, of the reported findings were likely to be exceedingly overstated or outright

With serious financial and scientific implications, apophenia can be incredibly dangerous. It might seem wrong, then, that we are still predisposed to believe in it. However, apophenia has a deep evolutionary history. Scientists believe that by encouraging pattern-seeking, apophenia could have been advantageous. As animals, we build mental models based on our past experiences that help dictate our future actions, and apophenia pushes us to find the patterns that underlie those results. By

identifying patterns, we can learn what to avoid, eat, trust, and mate with, which is evolutionarily advantageous. However, we may also link unrelated stimuli to those determinations. This is not unique to humans, nor just to animals. An AI trained to label photos of skin moles as cancerous or not began ascribing meaning to the presence of a ruler in photos, as it noticed that more of the cancerous mole photos it was trained on contained a ruler. This is a key example of apophenia extending beyond humans, as the model favored false positives, much like we do. Evolutionarily, this bias helped us steer clear of threats at the expense of being extra cautious instead of the reverse. This bias towards false positives increased the odds of survival and thus was selected for over time, leading to our current apophenia.

Nowadays, this tendency to ascribe meaning to the meaningless might feel a bit, well, meaningless, but whether on a scientific, financial, spiritual, social, or medical level, apophenia is one of the driving forces behind our decisionmaking processes. As we try to make sense of it all, it’s important to recognize the difference between desperate apophanies and the true epiphanies that satiate our desire for

Where Religion Lies In Science

By Caitlin Torralba

Illustration & Design: Caitlin Torralba

The relationship between science and religion has been subject to debate for many years. Both have very different approaches to how we can understand our world, one grounded on facts and evidence and the other reliant on faith and belief. Could there be an interdisciplinary approach that explains natural phenomena using both faith and science? Theologian Ian Barbour has proposed several dynamics that suggest the existence of a potential middle ground between these seemingly juxtaposing realms.

The conflict model views religion and science as fundamentally opposites of each other, acting as each other’s counterpart. Much of this arises when religious beliefs are interpreted in a literal manner, and scientific discoveries are often seen as a threat. One of the most famous cases of this is when Galileo proposed that the Earth revolves around the Sun, which at the time was deemed a heresy by the Catholic Church. Other concerns surround the teachings of evolution and creationism. For example, Stephen Hawking’s M-Theory proposes that many universes were created out of nothing without the intervention of a supreme or supernatural being. “Metaphysics”, from Introduction to Philosophy by philosopher and theologian Thomas Aquinas, counters this viewpoint through the idea of a First Cause or Prime Mover. What this means is that an uncaused and eternal entity is necessary for things to be set in motion, establishing proof of God’s existence. In religious texts such as the Bible, the Book of Genesis states that God created man and woman in his image. Many interpret this verse from the Bible to contradict Darwin’s famous theory on evolution, which proposes that species change over time, that new species come from preexisting species, and that all species share a common ancestor. Thomas Aquinas’s “Metaphysics” fails to acknowledge the mechanical nature of science, requiring a cause and event dynamic to explain earthly origins. Anyone who has also attended a school with any religious affiliation may understand the controversies surrounding evolution being taught in classrooms. Do we listen to what our faith tells us, or do we look at what science and what the evidence has to say?

Despite the countering theories and beliefs, other models seek a harmonious agreement between these two philosophies. The independence model holds the position that religion and science are different domains, asking very different questions based on ethical values and spiritual meaning versus empirical data. In other words, religion and science do not agree nor do they conflict with each other because they both discuss distinct aspects of the natural world. A good way to illustrate this concept is through explaining psychological versus religious counseling. One practice is based on

scientific and psychological principles, while the latter involves spiritual guidance and support based on religious beliefs. Both of these forms of counseling can be helpful depending on one’s individual’s preference or needs. Tackling different elements in human life, they are seen as two different, yet equally valuable, disciplines. Another approach is the integration model that acknowledges the value both science and religion bring to understanding what we see. Scientific questions of “how” consider the mechanical aspects, while religious questions tackle the “why” and other existential questions that pertain to our relationship to the world. In Islam for example, some scholars believe that the Big Bang theory aligns with Islamic concepts of universe creation and affirms Allah’s existence and creativity. It further demonstrates the harmony of religious beliefs and modernday scientific knowledge, promoting a more holistic understanding between scientific advancements and spiritual teachings.

Finally, the last two approaches invite more conversation between science and religion. The dialogue model proposes a mutualistic common ground. It encourages respectful, open-minded conversations between scientists, theologians, religious leaders, and other scholars to discuss how religious beliefs and scientific discoveries can influence each other. Faith is intrinsically a human way of viewing the world, just like biology and physics are. Andrea Barret’s Servants of the Maps explore this very topic: how do these two fields collaborate to account for the limitations both in science and faith? Scholars such as botanist Asa Gray and physicist-geneticist Francis Collins contributed to a more recent concept known as Theistic Evolution, which proposes that God or a supreme being set evolution into motion. This viewpoint of evolution being consistent with a divine being is one of the many ways that modern science integrates religious beliefs. An approach similar to the dialogue model is the conflict resolution model. The key difference with this one is that it acknowledges the past conflicts between religion and science, fostering them and emphasizing mutual respect between their ideas.

Overall, there is no singular answer as to where exactly religion lies with science. They are constantly evolving and adapting throughout the years, with discoveries being made and society undergoing changes in values and beliefs. It is important to promote healthy, open-minded conversations and respect for differing viewpoints, especially at the University of Miami where students and faculty alike come from many diverse backgrounds, cultures, and values.

By BellA Jimenez illustRAtion & desiGn: veRonicA RicHmond

Imagine an ant crawling on a basketball, placed in the center of a vast room. From the ant’s perspective, the ball is never-ending. Even if it manages to crawl all the way around the basketball and onto the floor, the room is a new challenge the ant must take on. Overwhelmed by the great unknown, who wouldn’t be confused by what lies beyond basketball? Consider now that we are the ant, our planet is the basketball, and the observable universe is the room. We have managed to navigate our way around the world and have begun venturing to other celestial bodies. Despite our species’ advances in understanding our surroundings, we still question what lies beyond the tangible world we inhabit.

For decades, scientists have made attempts to quantify the universe.

Astronomer Allan Sandage became the first person to come up with a reasonable measurement for how big the universe is, with today’s consensus being 93 billion light years in diameter – a number so large most people cannot even comprehend it. Perhaps we could invent technology that will allow us to travel at the speed of light, and say we then manage to travel from one “end” of the universe to the other. What happens then? Do we hit an invisible barrier and turn back around? This idea relies on the belief that the universe is finite. However, scientists have measured that the universe expands about 42 miles per second per Megaparsec, or 42 miles per second per 3.26 million light years. To put it simply, that is a lot of expansion per second, and galaxies are increasingly being distanced from our planet.

If we are to begin to fathom how big the universe is, we have to imagine it as a relatively flat shape. Pretend our basketball has turned into an 8.5” x 11” sheet of paper. In order to have this piece of paper expand, we add more flat pieces of paper to it. The same can be said for the universe. Presuming that the universe is mostly flat, cosmologists have been able to reason why expansion occurs the way it does; expansion is not uniform in all directions. Dark matter, the seemingly driving force for expansion, is clustered differently throughout the universe, possibly leading to different rates of expansion. This begs the question: what is the universe expanding to? If it were to be constantly spreading out in all directions, wouldn’t there be something being moved out of the way in order to make room for the incoming universe? There has to be something that exists in its place in the meantime. It’s a frightening concept, the existence of nothing beyond the universe, the very existence of nothing itself. We are taught that everything has a beginning and an end, so to be presented with the idea that the cosmos has no end, and maybe no beginning, goes against everything we’ve ever known and opens the door to an existential crisis. It torments the mind to try and comprehend something so abstract, at least to those of us who aren’t experts in cosmology.

The feeling I get when I wrap my head around the idea that the universe is infinite can only be described as unnerving. However, that is the humbling nature of the unknown. That is the same feeling that an ant has on top of a basketball, in the center of a room, unsure if a finite “end” is even real or merely a boundary to explain the inexplicable universe.

To Infinity, and Beyond!

Rain, Rain, Go Away

How Seminole Spirituality Helped Predict Natural Phenomena

By Jessica Weinberg

Illustration & Design: veronica richmond

In our modern world, weather forecasts are only a few swipes or taps away… and thanks to technological advances, these forecasts are now available at our fingertips, tucked safely away in our back pockets. These forecasts– predictions of our future– rely on an insurmountable amount of technology that, even now, continues to be refined. Radars, satellite imagery, and even manned aircraft that fly into the hearts of hurricanes all come together to form those integral apps and television segments we have come to rely on. But even with all this scientific progress and technology, we must acknowledge that these forecasts can still be incorrect. So, before technology came to aid us, how could people even begin to predict the weather?

The atmosphere is an incredibly complex system– one that is affected by a plethora of variables that tend to interact in unexpected and sometimes unpredictable ways. And for the Seminoles, an indigenous American tribe, this is especially true.

In the 1770s, the Seminoles officially established their roots in Florida, yet it didn’t take long for conflicts to arise. By the early 1800s, these conflicts escalated into wars against American

colonists trying to displace the Seminoles west of the Mississippi River. Seeking refuge in South Florida, they faced not only sudden weather changes but the prevalent threat of hurricanes, too.

An animistic tribe, the Seminoles believed that objects, natural phenomena, and even the universe itself had a soul. Weather, in their eyes, is something beyond their control, something that acts as its own sentient being. That said, as early as the mid-19th century, many Seminoles began to convert to Christianity, an effort mainly executed by the Southern Baptist Convention. In Christianity, many believed extreme weather events were a way of God punishing sinful acts–reinforcing the notion that weather is beyond human control.

Indeed, it is true that the weather is uncontrollable. It is impartial and indiscriminate by nature, and that was a lesson the Seminoles learned very quickly. So, while still maintaining their reverence for the spirits of the natural world, or praying to God, the Seminoles took weather prediction and preparation into their own hands. Many indigenous children were taught at a young age how to “read the signs” of nature– a crucial skill that helped to ensure their survival. The Seminoles, as well as many other indigenous tribes, knew that you could almost feel a bad storm coming.

The signs were clear to those who knew where to look. First, the winds would pick up, twisting and turning the leaves on tree branches to reveal their pale-colored undersides. Children would be told to look into the distance and then asked, “Can you see the rain?” By peering into the distance, it wasn’t uncommon to be able to see bands and streaks of precipitation. Another sign requires another one of our senses– smell. By taking a deep breath, the Seminoles could smell the rain coming, even if they couldn’t see it. Other signs relied on nature, and the Seminoles would rely on their cues. Birds would gather in trees, crickets would stop chirping, and seagulls would flock further inland… surefire signs of an impending storm.

For people who didn’t have easy access to a weather app, the

Seminoles were surprisingly accurate with their predictions, enough so that they could easily survive the sometimes unpredictable nature of South Florida.

We now know the rain these indigenous people saw is a meteorological phenomenon called “Virga”– observable streaks of precipitation. And the rain they smelled? Petrichor. When you can smell the rain coming, your sensitive nose picks up on the scent created by rain hitting soil, which creates a scented mix of ozone, petrichor, and geosmin.

The Seminole people’s connection with nature went beyond just surface-level weather predictions. Their lives were intertwined with their natural environment– they were hunters and fishermen who relied on changes in meteorology and climatology to survive. As time passed, the Seminoles adapted to new circumstances, and today, they have largely embraced Christianity while still preserving and observing many traditional aspects of their native religion. They incorporate modern-day technology and other weather forecasting methods into their lives, illustrating their ability to integrate contemporary tools with their historical practices.

With the seemingly infinite capabilities we have now, where knowing the future of weather can be done without a thought, the Seminole’s reliance on their senses and cues of nature seems wholly outdated. Yet, nature always finds a way to surprise us. So, next time you’re in need of a forecast, perhaps just relying on your senses can be just as handy.

The Intersection of Science and Poetry:

VERSES FOUND IN THE UNIVERSE

by Nicole

Vedder illustration & Design: veronica richmond

Art and Science seem like juxtaposed topics that are meant to be at odds with each other.

Poetry is the pursuit of our flights of fancy, of beauty through the artistic usage of words and structure, embodying humanity in its written intimacy. How would this ever be related to something as rigid as science? Science strives to understand the world around us through evidence and drawn out conclusions, while poetry attempts to understand the world through experiences and how we feel about the abstract ambiguity of the universe. While it seems that science and poetry are complete opposites, maybe both would benefit when the lines were blurred.

Whether it be science in relation to art, as some earlier poems in history were, or applauding the exploration of science as a subject in the written word, there is an intersection between the two. Unintentionally or not, poets have been intermingling the subjects of science and art for as long as we can remember.

The Scientific Revolution of the 16th and 17th centuries signified the rise of modern science and influenced the literature at the time. Inspired by the discoveries, or using them as cornerstones of controversy– writers, known as the late Romantics, had a lot to say. Many of the written works dealt with an analysis of society's changes due to the increase in knowledge from the discoveries in the field of science. Mary and Percy Shelley, Lord Byron, and Samuel Taylor Coleridge were all at the forefront of this phenomenon.

Some were opposed to this impact, such as Edgar Allen Poe. Poe bore witness to many monumental advances in science and technology in his lifetime, and in his famous “Sonnet to Science”, he denounces science as malevolent, accusing it of ruining art and creativity–

“Science! True daughter of Old Time thou art!

Who alterest all things with thy peering eyes.

Why preyest thou thus upon the poet’s heart,”

While he may have been pitting the disciplines against one another, he intermingled the two by commenting on science through his art which suggests that, perhaps, the two aren’t meant to be apart. The commentary of science, be it accusatory or laudatory, leads to a sub-genre that is defined by the content itself. “Science Poetry” articulates aspects of a certain field or views the topic that is to be written about through a scientific lens. This can be effectively done through vivid imagery and sensory details, the utilization of scientific language with literal and figurative meanings, the exchange of information that deals with the subject at hand, and the contrast of objective scientific language with the personal and intimate experiences of the speaker, yet still allowing the theme of the poem to be interpreted by the audience that reads it.

In "Ode to the Electric Fish that Eat Only the Tails of Other Electric Fish," by Thomas Lux he references electric eels and their biological characteristics,

“Without consulting an ichthyologist eels are fish I defer to biology’s genius.”

even the title and some verses in the poem refer to how they can turn cannibalistic and the comparison to how the feature of the organism is artistic:

“The need to hide while regrowing a tail teaches guile. They’ll eat smaller tails for a while.

These eels, these eels themselves are odes!”

I know that as a microbiology and immunology major, I sometimes put learned concepts into the context of a poem due to my fascination with the subject matter, or I start making scientific metaphors in my regular poems. The intersection is about merging the two subjects to create something truly beautiful. Below are some verses I have written, inspired by what I have learned through my courses and personal experiences.

“Diary Entry of a Virion, for when I feel Different”

Capsid Soul

Lysing Heart

Don’t Breath

Darling

Well, we are not seen as Living.

Sitting still Different space occu -pation Situation

Means that Sudden quiet Is not Alive.

If I Move about Different -ly, Rather, Not at all Am I Real?

“I mean, it’s only proper aseptic procedure” Make sure to sterilize the loop with red hot heat before you dip. Inoculate my thoughts.

“Blood Agar” Somehow You cause hemolysis in my bloodstream. You tend to eat up my blood cells Faster than they can revive themselves.

“Phytophotodermatitis ” I.

glass blowed dipping dots onto the backside of palms Liquid lava leaves dark spots in their wake Inkblots on my left hand Pointillism on my right Trying to make a companion warding off loneliness No other hands to hold Except themselves their self-made Artwork.

II.

The dots speckle on my hands Like the back of an egg But they hurt reminding me that the world spins harsher sometimes, If only a little. Omelets accidentally flipped onto the floor.

Nothing is as it Seems

The Science of Visual Perception

by brad ThompSoN

illuSTraTioN & dESigN: vEroNiCa riChmoNd

The world around us is an alluring, mesmerizing cascade of colors, hues, shapes, and patterns. An entire landscape of visual enrichment that lies outside the eyelid bounds. We could admire the beauty of the visual world for the rest of this article, but you don’t need me to tell you what you already know; you will experience that when you look up from this page. Let's take things in a slightly different direction through a question. You’ve undoubtedly thought of this or been asked this before, but what color is the “U” logo? Orange and green, right? If that's what you think… I’m sorry to say, but you’re not entirely correct. Now, it's not your fault that your brain is telling you to think that; that’s just what it knows and tells you to answer. The “U” technically doesn’t have a color; nothing does. The orange and green that you perceive

when looking at the “U” is simply a construction of thought from your brain that you intuitively understand as certain colors, from years of stimulus exposure and learning. Essentially, nothing you see in the visual world exists the way you have always understood it to. All things that exist in our world possess an innate ability to absorb and reflect the visible spectrum light, with varying degrees to each factor. The color of an object is the result of the beautiful interplay between the different wavelengths of the visible spectrum and the combination of light energy hitting our retina. Our world possesses every color possible and no color at all at the same time. Light exists as a type of radiation energy quantified on the electromagnetic spectrum, existing at a frequency we can transduce in the eye into visual information. Now, that might have been a little much to digest all at once, so let's break it down. This concept starts with the sun (the same results are produced by lightbulbs, fire, computer screens, etc. yet the sun best supports this explanation), which releases monumental amounts of energy, some of which constitute the visible light spectrum. The visible light produced by the sun strikes objects that absorb certain frequencies of this light and reflect others, a quality bestowed to them by the atoms they are made of. The light that is reflected by the object is what we take in and process as a form of sensory information. The frequency of light that hits our retina, the region of specialized sensory cells at the back of the eye, is turned into an

electrical signal in the brain. This signal will pass through multiple information-processing areas, allowing for one to process an object’s possession of color. Color is the result of reflected energies and their interpretation by our brains, therefore the world is realistically devoid of colors without our brains to understand and enjoy them. This is why if you’ve ever been in a pitch-dark room, objects don’t seem to exist without light, yet we know they are there through our other senses.

It wouldn’t be fair to neglect talking about the brain and the tremendously complex work it does to make sense of the overwhelming visual world we live in. Our understanding of the visible world is dependent upon our brain’s ability to absorb and

the world is realistically devoid of colors without our brains to understand and enjoy them.

process a myriad of stimuli every second and then turn that into a comprehensible stream of information. Opening your eye exposes the receptors in your retina to a continuous stream of information, and their job is to funnel this visual data to the brain for processing. Now, imagine trying to catch hundreds of tennis balls every second and, in addition to catching them, you must use them to build something, such as a house or statue. Seems impossible, right? Maybe, but this is relatively comparable to the second-by-second workload of the human brain, processing what the eyes are feeding it. The human brain is constantly being thrown bits of information that it has to integrate, sort through, and edit down into a usable stream of understanding. The reason I use the word “edit” here is due to another impressive facet of the brain’s information-processing capabilities. Much of the visual stimuli that we are exposed to is nothing more than noise, which means that the brain has to analyze all of the signals and make decisions to cut out and/or fill in the information, in order to stitch together one clear and fluid picture of our visual landscape. Ultimately, this powerhouse of an organ is responsible for giving the outside world the visual depth and beauty that we are so familiar with seeing, creating meaning and synergy out of nothing but signals.

Brain Organoids and Where Consciousness begins Brain Organoids and Where Consciousness begins

By Blake Goldberg

By Blake Goldberg

Illustration &

Illustration

HDesign:

Veronica Richmond

& Design: Veronica Richmond

uman beings are not special…Well, we all know that’s not quite true, but from a biological standpoint, it is. We are made up of the same essential building blocks of life as every other living thing on this planet. We share 60% of our DNA with a banana, 90% with dogs, and nearly 99% with chimps. Clearly, even those small differences matter, and at the microscopic level, are what makes us human. On the macroscopic level, several things make us human. We walk upright, have opposable thumbs, and have the most advanced and complex nervous system on the planet. The brain is the primary processing center of the central nervous system, and it’s only through the recent 20th-century advent of neuroscience that we know this. Moreover, we now understand that our brain controls our personality, holds our memories, and is responsible for our consciousness. We as humans believe that consciousness is an integral part of living, even more important than a beating heart. We are willing to go so far as to declare people “brain dead” and shut off life support when our brain no longer functions, showing that our society equates consciousness with life itself. The human brain is clearly special, which only makes it more complicated when we experiment with human brain cells.

In labs all over the world there are billions of living human cells. We experiment on them, grow them, kill them, do whatever

we want to them with no ethical dilemmas because we understand that humans are more than the sum of their parts (cells). However, as science advances, it gets more difficult to differentiate what is human and what is just a collection of cells. Organoids are three dimensional structures that are derived from stem cells, self-organize, and mimic the function of a real organ. The first human brain organoids were created in 2013 by a group of Austrian scientists studying microcephaly: a neurological condition characterized by an abnormally small head and underdeveloped brain . By generating brain organoids with genetic mutations associated with microcephaly, researchers were able to observe how these mutations affected brain development, cell proliferation, and the formation of neural structures in a way that closely mimicked the condition seen in some individuals with microcephaly. In December of 2022, a research team headed by Dr Brett J. Kagan, the Chief Scientific Officer at Cortical Labs, created human brain organoids akin to something out of science fiction. By using a combination of stem cells and mouse embryos the researchers were able to grow about 800,000 brain cells in a dish. This dish was divided into two sections: the sensory and motor electrodes. These electrodes allowed the “brain in a dish” to interact with a simulated environment. That environment was none other than the 1972 Atari classic: Pong.

spirituality the science of why humans

seek spiritual enlightenment

Spirituality is one term that has undoubtedly taken over modern culture within the past few decades. One study from the Pew Research Center showed that only 54% of Americans see themselves as religious, while a staggering 75% describe themselves as spiritual. However, what is spirituality? Spirituality defines how an individual discovers and fully encounters the world around them. Many confuse spirituality with religion, and, while there certainly are similitudes and they can overlay, they are not the same. Faith involves rituals, practices, and worship. However, spirituality does not include specific rules; it concentrates on the individual. The reality is that there is no one path to take when practicing spirituality; since it focuses on the individual’s journey, each person will discover their own way.

Spirituality can be traced back anywhere from 2300 B.C. to 1500 B.C. Indus Valley, where Hinduism was born. Although Hinduism is a religion, and thus seems contradictory to the definition of spirituality, it emphasizes the individual’s spirituality. Hindu practices describe three ways of practicing spirituality, also known as marga: Jñana (knowledge), Bhakti (devotion), and Karma (selfless action).

Similarly, Buddhists follow the Eightfold Path, a general guideline on liberating oneself from samsara: the never-ending cycle of rebirth, suffering, and death. The Eightfold Path is supposed to lead one who practices it to a state of nirvana or escape from samsara.

Mindfulness is the modern practice of spirituality. According to mindful.org, “mindfulness is the essential human ability to be fully present, aware of where we are and what we are doing, and not overly reactive or overwhelmed by what is happening around us.” One can practice mindfulness in a variety of ways. Countless amounts of people incorporate mindfulness into their daily lives by doing breathing exercises, slowing down their daily pace, and being more present overall. In this way, one can feel more connected to the world around them, the very definition of spirituality. Despite this , one must wonder if mindfulness and spiritual practices are just pseudosciences or if there is any scientific validity to them .

There are many studies about the science behind mindfulness and spirituality. One of the main goals of most who practice mindfulness is to reduce stress, and spiritual practices are one way to do that . One study published by Psychosomatic Medicine: Journal of Biobehavioral Medicine shows that mindfulness practices affect two different neurological stress pathways and change brain structures relating to emotion and attention. Another study, included in the Clinical Psychology Review Vol. 37, showed that people who practiced mindfulness and spiritual practices were less likely to react strongly to negative thoughts or react irrationally in times of intense emotion. So, we recognize that mindfulness is effective in reducing stress and promoting rational thinking, but how does this happen?

A study by researchers at the University of Pittsburgh and Carnegie Mellon University tested the effects of consistent mindfulness practices on individuals using MRI scans. They found

by: Gianni Echeverria

Illustration & Design: Vrinda Gupta

that after eight weeks of spiritual practices, the brain’s amygdala dwindles. The amygdala is often called the “fight or flight” center of the brain, and it belongs to the limbic system, one of the oldest and most primal parts of the human neurological system. It regulates extreme emotions like fear. Researchers also found that as the amygdala shrinks, the prefrontal cortex strengthens. The prefrontal cortex is the portion of the brain associated with high-level neurological functions. Now, not only does the brain structure change after the consistent practice of mindfulness and spirituality but how different parts of the brain interact are also affected. Connections between the primal parts of the brain, like the amygdala, and the rest of the brain weaken; conversely, connections between parts of the brain accountable for high-level functioning and the rest of the brain strengthen.

Mindfulness and spirituality allow for more high-level and advanced portions of the brain to supplant the primal brain when it comes to decision-making. It allows one to make more intelligent, more informed choices. This ability is critical within our modern society, with general stress levels at an all-time high. According to the American Institute of Stress, 94% of employed individuals report feeling chronic stress in the workplace. Considering how prevalent stress seems to be in our modern society and the devastating physical and mental consequences, spirituality and mindfulness practices are needed now more than ever.

physically changes the brain to better serve the needs of those who practice it. It reduces stress and allows the individual to better navigate difficult situations. As the primal brain weakens, the advanced brain strengthens. In a society where many people feel tired and overworked, mindfulness and spirituality have the potential to seriously help. Humans seek spiritual practices to soothe themselves from the stressors of society, and the research shows that it does just that.

UNIV ERSE US R

by Emily Danzinger

Illustration & Design: Veronica Richmond

Here’s your short breather after a slew of thoughtprovoking articles about our cosmic connections. Whether considering the possibility of parallel universes, how science ties into major religious beliefs, or if our consciousness, the very thing upon which we base our fundamental understanding of our world, is as concrete as we hope, it becomes increasingly apparent just how small we really are.

In reality, we - every single one of us - are insignificant. We don’t matter in the grand scheme of things. Our lifespans are yet a mere fraction of a blink in the universe’s eye. Anything that we do or say or feel, frankly, means nothing - we are indistinguishable on the scale of time and space.

Okay, take a real breather with me.

Deep breath in…..1…2…3…4

And out….1…2…3…4

In…1…2…3…4

And out….1…2…3…4

And yet, this insignificance should be viewed as anything but negative. We don’t matter, and that means neither do the things we worry about. Keep that in mind next time you stress about a major assignment or if you’re scared you were too bold when talking to your

crush. Take that first step, make that first move … you have nothing to lose, because none of it matters.

Even in such insignificance, though, we should not understand how simultaneously significant we are. We are made in the universe’s image. We are the universe. The glimmer in our eyes mimics the twinkle of stars. Our stretch marks mimic river routes, worn down over the course of several million years by subtle running water. Our very veins, our life force, mimic the root systems of trees many times our size.

And we each have a universe inside of us. The miracle of life, if you want to call it that, is dependent on billions of cells, on their coordination and collaboration and their doing what could be called their instincts until they die and new cells come into life over and over until our lives come to an end. Within us, we experience the cycle of life that we experience the very same way outside of our bodies. We live, we grow, we serve our purpose, we die - our children do the same and so do their children and so do their children and so on until you’re blue in the face. In so, the universe maybe cannot be the universe without us - not necessarily as individuals, but most certainly as a whole.

And I’m so glad to introduce some of our MIC 280 writers that look to further elucidate the parallels between the universe around us and the very functioning of our own body’s universe.

Antibiotics AND the Gut

By Jess Bucello

illustRAtion & desiGn: veRonicA RicHmond

Antibiotics, to this day, are one of the most important discoveries made by microbiologists and have been saving millions of lives since their first day of administration; antibiotics are essential for the treatment of bacterial infections. However, more recently, research regarding antibiotics and their effects on the microbiota are on the rise. It is believed that although they are effective in treating bacterial infections, they can also sometimes cause harm. The human body is home to more than 30 trillion bacterial cells, 99% of which reside in the lower gut, and are referred to as the intestinal microbiota. Antibiotic therapy can facilitate subsequent infections due to both the loss of colonization resistance in the microbiota and the overgrowth of unwanted microorganisms in the microbiota.

A healthy microbiome prevents colonization by foreign pathogens; antibiotic therapy can suppress commensal bacteria living within the host and significantly increase the risk of colonization and infection upon exposure to foreign pathogens. In a healthy individual, the gut microbiome protects against a wide range of invading pathogens, called colonization resistance. And a healthy microbiome can provide colonization resistance in many different ways - for example, microbes play an important role in deactivating toxic substances in food or made by pathogens, preventing pathogens from benefiting from the resources of the human gut, synthesizing essential metabolites, and assisting in digestion by breaking molecules down into short-chain fatty acids (SCFAs). The degradation of fibers into the short-chain fatty acids provides an important energy source for enterocytes (epithelial cells that line the intestines) that promote the antimicrobial function of macrophages and regulatory T cells. Additionally, the tight junctions between epithelial cells regulate permeability, allow only important nutrients to enter, and prevent pathogens from entering the portal vein. The portal vein carries blood that has important nutrients, which are metabolized in hepatocytes and stored in the liver, and plays a crucial role in immune and metabolic functions. If there is a disturbance in the homeostasis (balance) of the intestinal flora, called dysbiosis, the microbiota will be unable to function properly, causing one to become more susceptible to invading pathogens. The commensal bacteria is essential to the body's immune functions. Antibiotics are prescribed to target a specific pathogen causing a bacterial infection, but can have off-target

effects in which they can kill or suppress the growth of commensal bacteria, altering the levels of homeostasis in the gut microbiota, and therefore leading to an increased risk of a subsequent infection.

In a healthy microbiota, not only does the loss of colonization resistance due to antibiotic use increase infection risk, but antibiotics can also promote the growth of unwanted pathogens that are already present. In a healthy microbiota, there are both ‘good microbes’ and potentially diseasecausing pathogens. The ‘good microbes’ are referred to as obligate anaerobes, and secrete butyrate and other short-chain fatty acids to limit the availability of energy needed for the growth of the potentially disease-causing pathogens. Typically, these disease-causing pathogens are at a low abundance and do not cause disease in the microbiota. However, when antibiotics deplete the level of ‘good microbes’ they can lead to the overgrowth of these unwanted pathogens. Although dysbiosis is a leading cause of the growth of unwanted pathogens, the main mechanism by which potential pathogens grow is when they are more resistant to the drug than the ‘good’ microbes. If the harmful pathogens are resistant to the antibiotic, they will continue to grow. The overgrowth of these opportunistic pathogens can cause a local disease. Also, microbiota dysbiosis can lead to a weakened intestinal barrier, or reduced host immune defense, allowing these overgrowing pathogens to translocate to other body sites where they can cause disease, such as the bloodstream. Overgrowth within the intestine can lead to increased shedding in the fecal matter which facilitates the spreading to body sites via external routes. Although antibiotics can cause harm, it is important to realize that this issue is not due to the ineffectiveness of antibiotics, but due to the collateral damage that they can cause to the gut microbiota. Researchers are working to identify reasons as to why antibiotics can disrupt microbiota homeostasis and ways to combat the issue. It is believed that antibiotic-associated infections can be reduced by directly minimizing the collateral damage of antibiotics by restricting certain individuals to certain antibiotics, decreasing treatment duration, or using a mix of different antibiotics. Also, since the gut microbiota can differ from person to person, it is believed that a more personalized medical approach can decrease the negative side effects of antibiotics. Researchers also believe that the elimination of potential pathogens before antibiotic use can lead to a decreased risk of the growth of opportunistic pathogens.

Oral Microbiome by

alexandra moutafis

design: Alexandra Moutafis

Let’s face it, no one flosses every day. We get scolded by our dental hygienist for poor brushing, flossing, and overall oral health. When you rub the back of your teeth with your tongue after a dental cleaning, the clean ridges between each tooth feel smooth and defined. As time goes on, the space narrows and a course film, otherwise known as plaque, forms. What is this bio plaque buildup and why is keeping a good oral cleaning regimen so important?

The cells and bacteria living in your mouth, also known as the oral microbiota is diverse and play a major role in one’s mouth and overall health. Living in one of the three distinctive habitats, supragingival plaque, buccal mucosa, or tongue dorsum, the oral cavity is home to many bacteria, bacteriophages, fungi, protozoa, archaea and human and eukaryotic infecting viruses. Factors influencing the microbial community composition at distinct sites include the surface characteristics of the substrate, gradients of oxygen and nutrients, and proximity to salivary glands. Genera such as Fusobacterium and Veillonella, and families such as the Prevotellaceae, contain separate, distinct species that are specialized for the tongue, dental plaque, or gums, suggesting that the oral microbial community has evolved to occupy these distinct oral habitats.

To identify these microorganisms, people use gold-standard detection methodologies including cultivation, sequencing and bioinformatics, and microscopy and fluorescence-based cell sorting. Visualizing the spatial organization of the oral microbiota shows differing taxa, strain levels, and species across each area of the mouth and the distinct footprint of each person’s oral cavity can be used to identify individuals. There are similarities and differences between everyone’s mouth, but one thing is certain: there is still a lot to discover and explore regarding the organisms that live there.

Most microorganisms that live in these habitats benefit from us through a commensalistic relationship. Recent advances in oral microbiome research like CLASH-FISH imaging have revealed the spatial organization or biogeography of oral biofilms, which determines which bacteria are located in close enough proximity to influence each other’s biology and determine emergent biofilm properties. For instance, the common mycobiome Candida who consumes sugars survives with the help of Streptococcus gordonii aiding in its escape from macrophage phagosomes that gobble them up like

illlustration: veronica richmond

Pacman. However, recent research indicates that phages are exerting significant selective pressure on the oral microbiome. Although they are very sensitive to environmental conditions, studies of oral phages have shown that they can impact overall community assembly and interactions with the human host. Identification of these phages is made possible through improved sequence databases, sequencing capacity, and phage-detecting bioinformatics tools like CRISPR.

Maintaining good oral hygiene combats and prevents oral and systemic diseases. As we continue to investigate and learn about the oral microbiome, we discover bone-chilling facts about how it can negatively affect our health. More recent analyses have discovered that the main culprits are contributors to inflammation in different areas of the mouth. Disrupting the normal conditions or homeostasis of the oral cavity triggers a change in the microbiome and host. This causes an immune response, specifically inflammation, that leads to illnesses and diseases like gingivitis and periodontitis. Recent studies have revealed the prevalence, abundance, and active processes in microorganisms that may influence ongoing inflammatory responses in chronic periodontal disease. P. gingivalis proteins promote inflammatory activity and plaque accumulation and are linked to Alzheimer’s disease and tau protein degradation. Filifactor alocis, Peptoanaerobacter stomatis, and Saccharibacteria are potential periodontal pathogens. Due to its ability to form biofilm and produce acid while being acid-tolerant, S. mutans was marked as a primary aetiologic agent of dental caries which is linked to a dysbiosis of the dental plaque microbiota. Other acidophilic organisms, such as lactobacilli and Veillonella, have also been associated with dental caries. Inflammation and disruption of periodontal epithelial barriers lead to bacteremia and systemic dissemination of oral bacteria which can have significant consequences at distant sites like bone marrow, cardiovascular tissues, brain, and liver. However, not all oral bacteria are bad. There are also many bacteria linked to good dental health like nitrate-reducing bacteria. Some examples include taxa within the genera Rhia, Neisseria, and Haemophilus. Investigating nitrate as an anticaries prebiotic and nitrate-reducing bacteria as anti-dental caries probiotics will hopefully lead to new preventive modalities that synergize with oral hygiene and fluoride treatments.

The Hidden Heroes of Forests

illustRAtion &

By liz mAzzie

desiGn:

veRonicA RicHmond

Picture a nice healthy forest. Pretty, right? While you may be picturing the trees and animals, the ecosystem of a flourishing forest is not seen in the leaves or the creatures that live in these habitats. Often, the most crucial factor to a flourishing ecosystem is what we cannot see. Deep in the soil are living organisms that are the backbones of thriving environments. These living organisms help make up the forest’s microbiome - a microbiome is the group of microorganisms, like fungi, protists, bacteria, viruses, and archaea, that reside in a particular area. They reside beneath your feet, in the soil and attached to the roots.

In comparison, the gut is the location of the microbiome in a human, and this contributes to the immune system, and food cravings as well, which is why you need to take your probiotics. The forest microbiome is similar, it essentially controls how an ecosystem functions. It works alongside the plants, aiding in nutrient cycling which is essential for ecosystem survival. Now, I know what you're thinking, viruses? How would these be helpful and why are they there? I really wish we had an answer for that question, but it is unclear why they are present in these forest microbiomes. As for its importance, why would you care? Well, everyone and their mother knows that climate change is affecting the world around us, with deforestation being one of the leading factors. The forest biome used to be an incredibly diverse system containing different animal and plant species, and the decrease of these habitats has directly impacted the ecosystem. However, what about the microbiome associated with forest ecosystems? There are several different forest microbiomes, and the

drier territories (temperate and boreal forests) can be a hard place to find nutrients during those long winter months.

Microbiota in forests (bacteria and fungi) have been drivers of nutrient availability and cycling in these ecosystems since the dawn of time (or forests). This exchange is positively symbiotic between the micro- and macro-organisms that reside there. Plants provide for their pathogens with sugars and a host for the microorganisms to live on, and the fungi/bacteria provide an enlarged root system to find nutrients and water farther away than the root system could before. These systems, however, can only handle so much adversity. When the microbiome takes a hit, so does everything it is friends with. The trees die quicker, the animals in the trees leave, it’s all a big domino effect. So, just as you must take care of the bacteria in your gut, the ecosystem must sustain their microbial components, otherwise they are in for a seriously rough ride. In this day and age, however, it is becoming increasingly difficult for an ecosystem to flourish. Droughts, fires, increases in carbon dioxide, global warming events, nitrogen deposition, pest outbreaks…need I mention more? These ecosystems are being constantly kicked while they are down, and they cannot take much more.

Boreal forests, which have drier and longer winters, are dangerously susceptible to droughts. Warming is also negatively impacting these areas as it is shifting their usual habitat; however, there are some events that are actually helping these ecosystems in a minuscule amount. Since boreal forests are nitrogen-limiting, nitrogen deposition is allowing for the microbiota of this area to thrive. This can occur from sewage pollution, which allows for excess nutrients to

enter the biome.

Temperate forests, on the other hand, are hit with almost every combination of climatic changes possible. Decreased precipitation and increased frequency of fires is the first punch. They deplete these forests from their structure and basic needs. Then the trees will think they’ve had enough, but the uppercut of insects and pathogens hits those trees like a brick. Declines in growth and forest mortality rates in these regions have been observed due to these changes. Tropical forests hate droughts as well - they are quite literally called rainforests, so it doesn’t take much to infer that they need copious amounts of water. Fires are, not surprisingly, also a concerning factor. Additionally, fire recurrence is a real thing. Once they start, they tend to want to come back. Fires destroy microbiomes,

limiting nutrient availability, and thus preventing a speedy recovery after a burning. On a good note, though, plants containing a special type of fungi, called ectomycorrhizal fungi, are able to live in the decreased nutrient environment followed by fires, which allows them to become more frequent in these ecosystems, potentially providing areas of life that won’t be as affected by forest fires in the future.

The microbiomes in forests are under serious pressure with all the climatic challenges they are facing. But is it too late? Should we just give up? NO! That's not the answer - we should not give up on microbiomes because they aren’t giving up on themselves. They have been seen to adapt in these conditions. For example, droughts are actually not affecting fungi as they do bacteria, ever so slightly. Fungi are able to spread out, finding water and providing it to their symbiotic partners in crime. This does not mean that they are resistant, they just have a backup plan; they ultimately cannot last in extreme droughts. Studies have also been starting to observe fire-adapted fungi, which can improve the recovery time of a burned ecosystem. Another good thing is that elevated carbon dioxide levels are not damaging the microbiota since the carbon dioxide concentration in soil is often higher than the atmosphere. Even in the face of such positivity, don’t let this information lead you to think that these ecosystems are not crying for help. Even if they were able to sustain all but one of the damaging impacts on these ecosystems, the microbiota would still be in trouble, which is bad news for our forests. Forests need the microbiota more than the microbiota needs them, honestly. So, if you take anything away from this article, make it that the microbiome of forests is critically important and, as climate change continues to beat them down, they find it harder to provide for the trees. Like the effects of eating bad food on your gut, the forests get “stomach problems'' when their microbiota isn’t plentiful. So, care for the microbiota, show them some love, because they need more appreciation in this world full of climatic disasters.

The Ties Between Forests and Us

by Zuri Patel illustration & Design: veronica richmond

Close your eyes and try to picture a lush and vibrant rainforest. What do you see? An abundance of green trees and plants? Monkeys and birds and poison dart frogs? Waterfalls and rivers? Whatever you picture, its surely rich with life and diversity. This may come as a shock, but your mouth is just like a rainforest. There are billions (yes, billions) of microbes living in the mouth that can significantly impact the overall health of one’s body. Advances in technology and detection techniques have recently brought light to the vast diversity of the oral microbiome. Just like the plants and animals of the rainforest, oral microbes also have their niches within the mouth, and if they get out of balance, they could cause serious diseases both in the mouth and the rest of the body.

So, what are these microbes exactly? The human mouth houses millions of bacteria, viruses, fungi, amoebae, and archaea. Among these, bacteria are the most prevalent and have the largest biomass out of all the other oral microbes. Over 700 different species of bacteria can be found in the oral cavity, and the most prevalent ones are found in a large percentage of people. Candidate phyla radiation (CPR) bacteria is one of these groups, and Saccharibacteria is the most prevalent of the CPR bacteria. Research has shown that large amounts of Saccharibacteria is associated with oral diseases, such as periodontitis.; however, other studies have discovered that Saccharibacteria can actually keep other pathogenic bacteria in check, which is helpful for the host.

Viruses of the oral microbiome primarily consist of bacteriophages, which are viruses that infect bacterial cells. Although they are not the most prominent, researchers have discovered over 60,000 different bacteriophages that reside in the mouth. More

research on the impact of bacteriophages is needed, but a few studies have noted selective pressures driven by these phages. Additionally, there also exists viruses that can infect human cells found in the human saliva of over 90% of the human population, such as Herpesviridae that can lead to periodontal disease.

Fungi are not as prominent in the oral microbiome, but Candida and Malassezia are the most abundant. These fungi can interact with oral bacteria to then cause oral diseases, such as caries and tooth decay.

The least abundant microbes are the archaea, amoeba, and flagellates. Despite this, these are still pathogenic and can be linked to periodontal disease.

Just like animals that live in a specific layer of the rainforest, oral microbes like to live in specific niches too. Some find the enamel warm and cozy, while others prefer the tongue, or specific regions of your gums. What’s interesting is that some microbes of the same species (like Streptococcus) may prefer different niches. You may be wondering why there is so much variation in where microbes like to live - this has to do

how the amazon and our mouths compare

middle of the rainforest and starts disrupting the natural cycles of the forest, effectively depleting resources used by the local environment. This demonstrates how some of the most common oral diseases arise. For example, dental caries, or cavities, are linked to an abnormal increase of acid-tolerant microbes that produce biofilms and acid. Scientists have identified a few species, such as S. mutans and C. albicans, with these properties, but more research is needed to determine their full effect. Interestingly, a few bacteria have been recently discovered to have anti-caries properties via their ability to reduce nitrate.

with the fact that each microbe has a unique surface, and each surface reacts differently to the varying levels of oxygen and nutrients in different places of the mouth. Think of why monkeys mostly live in the canopy layer of the rainforestthis is where they can find the most fruit and leaves for their diet! Of course, this site specialization phenomenon is not so cut and dry, as there are not strict barriers separating the different areas of the mouth (monkeys like to wander, too). Saliva spreads all over the mouth and often picks up microbes and drops them off in a different spot. So almost all microbes can live in the saliva, but the majority of the “pack” stays in their niche. Researchers have been able to make these discoveries by combining existing methods with new technology. They are able to actually visualize the biogeography of the oral microbiome by making each microbe a different color through a process called “spectral imaging fluorescence.” CLASI-FISH is a more advanced imaging technique that allows researchers to identify organisms of different taxa and species at the same time. This allows them to see which oral microbes are pathogenic or not.

Now picture this: an invasive species is dropped off in the

Periodontal disease is also caused by a disbalance, but between the oral microbiome and host immune cells. Immune cells are regularly present in the periodontal pocket and usually have a healthy relationship with the surrounding microbiome; however, any shift in this balance can cause increased inflammation and potentially lead to gingivitis and periodontitis. Some studies have compared the progression of gingivitis in affected patients and noted that there are three types of inflammatory response - high, low, and slow. Each of these responses is due to a specific genotype, suggesting that both host and microbial genetics contribute to the development of gingivitis.

The story behind the development of oral cancers is no different. About 90% of oral cancers are linked to non-phage viruses, most notably HPV and Epstein-Barr virus. Aside from viruses, studies have shown that a fungus, C. albicans, is also associated with oral cancer. Not only can a non-homeostatic oral microbe lead to cancer and diseases in the mouth, but it is also associated with diseases throughout the rest of the body. Studies have linked certain oral microbes (specifically those living in the periodontal pocket) to diseases occurring elsewhere in the body, including Alzheimer's, inflammatory bowel disease (IBD), and diabetes. These diseases can develop when the periodontal microbes either travel to other parts of the body or cause too much disbalance, resulting in indirect effects.

Rainforests and mouths have a lot in common. They both require balance amongst a significant amount of players in order for their residents to thrive. Although unfortunate in some cases, it’s fascinating how interconnected the human body is. Research has already given scientists a clear picture of the influences of the oral microbiota, but more investigation is needed to apply these findings to real-life applications.

Gut Bacteria Breakout

By JARet fensteRstock illustRAtion & desiGn: veRonicA RicHmond

What if I were to tell you that one half of the cells in your body aren't even your own? Well… I would actually be lying. While it can vary from person to person, it’s estimated that the number of bacterial cells in the human body actually outnumbers the amount of human cells, meaning that bacteria make up OVER 50% of the total cells in your body. While these bacteria can be found all around the body, there is one place in particular where microorganisms like bacteria love to hide: the gut.

The gut is home to trillions of microorganisms. In fact, around 95% of the human body’s microbiota reside in the gut, outnumbering the amount of actual human cells by 10 to 1, meaning that for every one human cell, there are roughly ten microbial cells in the gut. While this fact may make you quiver, the truth is that most of these microorganisms are harmless or even beneficial to our health. However, there are some bacteria that can cause serious infections in the gut, such as Salmonella, Shigella, Campylobacter, and Escherichia coli. These bacteria can not only damage the gut lining, but also escape into the bloodstream and invade the microbiomes of other organs, causing life-threatening complications. How can they do that? And what are the

consequences?

First, let's get to know a little more about one of the most important aspects of the gut: the gut lining. An incredibly complex and dynamic structure, the gut lining separates the inside of the gut from the rest of the body. It consists of a single layer of epithelial cells (the same type of cell that makes up the outer layer of the skin) that are tightly connected by structures called tight junctions. These tight junctions work like a “velcro” or “zip-lock” system to fasten adjacent cells together tightly, and are extremely important for maintaining the structural integrity of the gut lining. The epithelial cells also secrete mucus and antimicrobial peptides to prevent the attachment and invasion of pathogens. These antimicrobial peptides work asyour body’s own tiny warriors, and are deployed to attack and destroy invading germs. The gut lining also has immune cells and sensory nerves that can detect and respond to foreign invaders.

Now that you know more about how the gut works, let's look at some of the deceptive and ingenious strategies that some enteric (or gut) bacteria have evolved to overcome the gut lining’s defense, causing damage to the epithelial cells. One great example is the utilization of type III secretion systems (T3SS). T3SS are needle-like structures used by

some bacteria to inject toxins or proteins into the epithelial cells. This system works sort of like a “molecular syringe”, and, once the material is injected into a host cell, the bacterium can essentially hijack the host cell’s machinery, creating an ideal environment for the bacterium to multiply. This injected material can also alter the tight junctions connecting epithelial cells, induce fluid secretion, and activate inflammation, resulting in health complications such as diarrhea, bleeding, and ulceration.

Some bacteria can even invade and multiply inside the epithelial cells, or cross the epithelial layer and reach the underlying tissue. When the gut barrier is breached, various substances can leak into the circulation and extra-intestinal sites, or anywhere outside the gut. These include host factors, such as blood cells, plasma proteins, cytokines, and hormones; microbiota components, such as bacterial cells, DNA, and metabolites; and pathogens and their secretions, such as toxins, antigens, and virulence factors. These substances, once leaked, can cause inflammatory responses, activate coagulation pathways, and disrupt organ functions.

Some enteric infections can also impair the host’s ability to regenerate the damaged epithelium. For example, some bacteria can inhibit intestinal stem cells, which are responsible for replenishing the epithelial cells. Interestingly enough, different bacteria have actually evolved independent ways to go about this, some of which include producing toxins that interfere with stem cell function, competing for resources that are crucial for stem cell development, and altering the local microenvironment, making it less hospitable for stem cell activity to occur. Some bacteria can also disrupt epithelial differentiation, or the process by which epithelial cells take on different roles in the gut, which is essential for maintaining the diversity and function of epithelial cell types. Some bacteria can even alter the composition of gut microbiota, which can affect the epithelial metabolism and immunity. In other words, these bacteria can negatively change the way your body digests and processes food and fights off infections.

Unfortunately for us, some enteric infections can have severe and long-lasting effects on the body. For instance, sepsis, a lifethreatening condition, can develop when the body's response to infection leads to organ dysfunction or failure. Another example, reactive arthritis, may arise after an infection in another part of the body, such as the gut, and can cause inflammation in the joints, eyes, skin, and urinary tract. Guillain-Barré syndrome, though rare, can also occur. This may result in the immune system attacking the nerves, causing muscle weakness, numbness, tingling, and paralysis. Inflammatory bowel disease, a chronic condition, leads to inflammation in the digestive tract, resulting in symptoms like diarrhea, abdominal pain, weight loss, and malnutrition. Lastly, enteric infections are also associated with an increased risk of colon cancer, which originates in the large intestine and can lead to bleeding, anemia, obstruction, and metastasis.

Hopefully all of this talk about bacteria, microorganisms, and the gut didn’t scare you away, but allowed you to realize the wonders of the micro-world, and gain a new appreciation for life of all sizes. While, yes, some gut bacteria can occasionally pose challenges, it is

important to remember that the majority of our gut microbes are key allies in maintaining our everyday well-being. They play a crucial role in our digestion, immunity, and overall health, ensuring that our bodies can thrive and flourish. Together, with a balance of these beneficial microorganisms, we unlock the potential for optimal health and vitality.

Chlamydia Transmission

By leAnnette GARciA

illustRAtion & desiGn: emily dAnzinGeR & veRonicA RicHmond

One of the major causes of sexually transmitted infections is a bacteria called Chlamydia trachomatis. C. trachomatis is an obligate intracellular bacterium that frequently goes undetected as it sometimes does not produce symptoms, which facilitates its spread throughout the community. When invading the host cell, Chlamydia are able to develop and multiply in membrane-bound compartments called inclusions. In unfavorable conditions, C.trachomatis enters a dormant state followed by the development of enlarged abnormal bodies that allow them to remain in the host cell until reactivation. When reactivated, these bodies go back to their developmental stage and begin to reinfect cells. Successful reinfection is reliant on host-derived nutrients and the bacteria's ability to disrupt host cells' metabolic pathways. This ultimately interferes with the physiology of the host cell.

This pathogen's entry into the host cell is a multistep process. First, C.trachomatis binds to the host cell's outer membrane protein called MOMP. Here, many interactions between the host cell and the pathogen take place to initiate a signaling pathway, which then triggers endocytosis. Through the use of axenic medium, C. trachomatis was revealed to form peptidoglycan rings for their replication process as they go through a budding process instead of binary fission for cell division. C. trachomatis needs to transition from a reticulate body, having a net-like formation, to an elementary body for survival outside of the host cell. In this elementary stage of C. trachomatis, DNA is more densely packed and the bacteria itself is smaller and more robust. This process is mediated by a protein called Hc1, which down-regulates gene expression, thus creating compact DNA. There are two models that propose possible stimuli triggered for the transition of these two states, the control dependent

model and the size control model. The control dependent model proposes that the reticulate bodies are closer to the inclusion membrane and loss of contact would result in the inactivation of T3SS, type III secretion system. The size control model proposes that reticulate bodies become smaller during replication until reaching a certain threshold initiating the transition into the elementary body.

For nearly 40 years, C. trachomatis was thought to be an energy parasite until sequencing of its genome uncovered surprising information. It was discovered that ATP is generated through oxidative phosphorylation as well as from glycolysis. In order for these processes to occur, it needs to skillfully take up a sugar called G6P from the host cell and use it as its main energy source. Although this is true, C. trachomatis is unable to use G9P during the rapid replication process because it consumes it for the synthesis of lipopolysaccharides, or LPS for short. In turn, these elementary bodies directly use host ATP to replicate. And not only does C. trachomatis feen on host ATP, it also steals amino acids, glutamine, dicarboxylates, iron, cholesterol, and other eukaryotic lipids to be able to run its bipartite metabolism, growth, and development. It does not stop there as C. trachomatis also actively manipulates the nutrient flow from the host by reprogramming cellular metabolism through modulation of central signaling pathways.

Host cells are equipped with mechanisms that target intracellular pathogens for self-defense. The first line of defense in cells is the pattern recognition receptors (PRRs), which identify pathogen-associated molecular patterns (PAMPs) or danger-associated molecular patterns (DAMPs). DAMPS are stress signals released by the host cells to indirectly sense pathogens. But one of the main mechanisms used for detection is the use of autonomous defense, autophagy and lysosomal degradation. Interestingly, C. trachomatis is able to avoid being targeted for autophagic destruction by preventing ubiquitination of its inclusion. Another host defense

is apoptotic cell death. Even so, C. trachomatis has evolved to be able to hinder apoptosis during the early replicative state, but possibly induce necrotic cell death in the infection process to escape from the cell. This manipulation involves multiple cell factors, proteins and interactions with the chlamydial outer membrane proteins.

There are many people who go untreated for Chlamydia because they experience no symptoms. This asymptomatic nature can be explained by the bacterium's interactions with immune cells. C. trachomatis is able to actively suppress the host’s immune response mediated by neutrophils through the chlamydial proteaselike activating factor (CPAF). CPAF renders neutrophils inactive by cleaving the peptide receptor on the neutrophils surface which prevents the attack on the bacteria by neutrophils. Monocyte-derived macrophages also play a role in immune defense. They are recruited at the site of chlamydial infection, most often in the genital mucosa, and are phagocytose or engulfed by macrophages. After engulfment, chlamydia is inactivated but some survive and remain infectious for several days. Due to the nature of phagocytosis of macrophages, they have become a microbial ‘Trojan Horse’, as infected macrophages may allow for C. trachomatis to infect other body sites and cause disseminated infections. C. trachomatis can enter a persistent state in response to various inducers such as tryptophan depletion and IFNy treatment. This is a concern as persistent C. trachomatis infections can lead to long-term tissue damage and contribute to the pathogenesis of chlamydial diseases, explaining why it is very important to remain up to date with STD testing. Chlamydia trachomatis is a very compelling and smart bacteria that is able to establish itself in the hostile cellular environment. It manages to survive by being dependent on host metabolites and protecting itself from the host's immune defenses. Through the use of effector proteins, its inclusion is definitive. While in the host cell, researchers have made progress in understanding the metabolic reprogramming of the host cell and how this affects the cells defense mechanisms as well its effect on the innate immune response. Models have also been developed, such as the use of pluripotent stem cells, to provide insight into how Chlamydia trachomatis establishes a long-term infection in the host. Although many questions have not been answered on the mechanisms C. trachomatis uses for long term invasion and replication, research in this field is advancing for the development of vaccines and therapeutic approaches.