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 ====== 5. Chemical Age ======
-**Juno:** Our boat is now moving from the Brahmaputra into the Jamuna, this is just the right time to start talking about the Chemical Age, because through Krishna of Mathura and the Taj Mahal of Agra the Jamuna has a profound symbolic connection with life. But to begin this age we need to brush up a little on Earth’s 4.5-billion-year history, because the first 4.0 billion years of it will be our terrestrial Chemical Age.
-**Socrates:** So in the Chemical Age we will focus only on Earth?
+===== - Timeline =====
-**Juno:** Since we know the history of complex chemistry on only one planet, it is logical in this age to think about Earth. But at the end of the discussion we will also talk about ways of searching for complex molecules and life on other planets, inside or outside the Solar System. In fact, our plan here is quite similar to that of the Planetary Age. In the Planetary Age Hermes mainly focused on the Solar System, but in the end he also spoke about the discovery of planets around other stars.
+<html>
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Chemical Age Table</title>
+</head>
+<body>
-**Socrates:** Good plan. Then begin.
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-===== - Seas and Atmosphere =====
+        #doku-cosmic-light {
-**Juno:** About 4.5 billion years ago Earth was born. For the first 500 million years the surface was very hot and full of volcanoes, and it spun very fast on its own axis, taking only 12 hours for one rotation. On top of that, many leftover pieces of rock and comets from the construction of the inner four planets kept crashing onto Earth from space during the Late Heavy Bombardment. This period is called the Hadean Eon. Some intact zircon (ZrSiO$_4$) crystals from that time have been found, from which we understand that oceans already existed then.
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-**Socrates:** How did the oceans form?
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-**Juno:** Through volcanoes and all the cracks in the crust, water vapor rose from inside Earth into the atmosphere, this process is called outgassing. After Earth cooled, this vapor formed clouds, and clouds produced rain. One reason for the oceans is this rain. But a large part of ocean water probably also came through asteroids and comets during the bombardment. At that time the whole Earth was probably surrounded by ocean, with no large continents. Scattered across the ocean were volcanic islands, the peaks of various volcanoes. There was oxygen in vapor and water, and oxygen in zircon, but there was no free molecular oxygen (O$_2$) in the atmosphere at all.
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-**Socrates:** Is the rise of oxygen in the atmosphere what this figure shows?
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-{{:bn:courses:ast100:oxygen.webp?nolink&800|}}
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-**Juno:** I am showing not only the increase of oxygen in the air, but also important changes in the chemical composition of the oceans. After the Hadean, the Archean Eon began 4.0 billion years ago. But Earth’s crust began to stabilize around 3.8 billion years ago, when the precursors of today’s continents, various microcontinents, started forming. In the figure you can see that many important events took place 3.5 billion years ago. At that time there were microbial mats, that is, layered colonies of cyanobacteria on the surface of the ocean water. The top layer of cyanobacteria had already begun producing oxygen by combining sunlight, carbon dioxide, and water, a process called photosynthesis. Over time these mats thickened and eventually turned into rock, known as stromatolites. By analyzing stromatolites we have learned how long ago free oxygen first began to be produced.
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-**Socrates:** On the X axis the figure shows time, but on the Y axis it does not show oxygen content directly, it shows the contribution of oxygen to atmospheric pressure, where 1 means 100%, 0.1 means 10%, 0.01 means 1%. Does this basically indicate oxygen concentration?
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-**Juno:** Yes, you can take it that way. At present oxygen makes up about 21% of the atmosphere, and it began to rise from zero around 3.2 billion years ago, where the dashed line starts. The earliest photosynthesis was not oxygenic, meaning it did not produce oxygen. At that time bacteria mixed oxygen with iron and water to form iron compounds on the ocean floor. Oxygenic photosynthesis began properly around 3.0 billion years ago. At the same time microcontinents were joining to form various continents. The newly produced oxygen reacted with iron on the seafloor, filling the oceans with iron. In the figure this is what is meant by “Iron Ocean.”
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-**Socrates:** From the figure it seems that for a long time after free oxygen began to be produced the amount of oxygen in the atmosphere did not increase. Oxygen production began about 3.1 billion years ago, but the Great Oxidation Event happened 2.1 billion years ago. For almost a billion years did oxygen in the air fail to rise because of the iron in the oceans?
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-**Juno:** Yes, iron was one reason. Another reason may have been microbes in the ocean that lived by metabolizing oxygen. Only after the amount of oxidizable iron in the ocean decreased did the oxygen produced by cyanobacteria start mixing into the air, and in a very short time oxygen in the atmosphere rose to nearly 1%. Because of this oxygen, sulfur was oxidized and began to mix into the ocean, giving us the “Sulfide Ocean.” How oxygen rose from 1% to 20% is a subject for the Biological Age, not now.
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-**Socrates:** Then now go back to the beginning of the Chemical Age. You have mentioned zirconium, silicon, oxygen, iron, sulfur, carbon and many elements. But we know that after the Big Bang the universe mainly produced hydrogen and helium. Where did all the other chemical elements come from?
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-===== - Periodic Table =====
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-**Juno:** Before understanding where they came from, we need to look once at the periodic table. The pier you see on the left is actually in Shakhahati Char, in the middle of the Jamuna. If we dock the boat at that ghat we will see a marvelous seven-story building that has been built in the form of the periodic table.
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-**Socrates:** Then let’s go.
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-**Juno:** Now you can all see it, the seven-story building faces the Jamuna, and each floor has 18 rooms. The top floor is number 1, and the very bottom one is number 7. From room number 3 on the bottom two floors, a two-story pier extends out toward the river. This pier is where the boat can be docked.
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-[The boat docks. Socrates and the other seven admire the building while still sitting in the boat.]
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-**Ishtar:** Then by showing us the building, explain the beauty of the periodic table.
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-[[https://pubchem.ncbi.nlm.nih.gov/periodic-table/|{{:bn:courses:ast100:periodic-table.webp?nolink|}}]]
+    <div class="timeline-table">
+        <!-- Row 1 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">10.5 – 11 Gy</div>
+                <div class="col-title">Synthesis of Prebiotic Molecules</div>
+                <div class="col-toggle">
+                    <svg viewBox="0 0 24 24"><polyline points="6 9 12 15 18 9"></polyline></svg>
+                </div>
+            </div>
+            <div class="t-content">
+                <div class="t-content-inner">
+                    In the highly energetic and volatile environment of the early Earth, the stage was set for the universe's transition from inorganic chemistry to the foundational building blocks of life. The primordial atmosphere, rich in simple gases such as methane, ammonia, water vapor, and carbon dioxide, was continuously bombarded by fierce ultraviolet radiation from the young Sun and intense electrical storms. These extreme energy sources catalyzed complex chemical reactions within the "primordial soup" of the early oceans. Through these spontaneous interactions, simple atomic constituents were forged into complex organic molecules, including a diverse array of amino acids and nucleotide bases. This crucial synthesis demonstrated that the essential components required for biological life could assemble naturally under abiotic conditions. It marked the dawn of the Chemical Age, a period where matter began to organize itself into increasingly intricate molecular structures, laying the essential groundwork for the subsequent emergence of self-replicating biological systems.
+                </div>
+            </div>
+        </div>
-**Juno:** Each floor is a period (row) of the periodic table, and each room is a group (column). Since there are 7 periods, there are 18 groups. The columns can again be divided into four blocks: s, p, d, f. The first two columns make the s-block. In this block hydrogen is a nonmetal, besides that the first column are alkali metals (red), and the second column are alkaline earth metals (purple). Helium in the last column is also placed in the s-block. Except helium, everyone in columns 13 to 18 are in the p-block. Among them are metalloids, post-transition metals (green), halogens, nonmetals (yellow) and noble gases (brown). A few of these nonmetals are very important for life, especially carbon (C), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S), abbreviated as CHNOPS. Columns 3 to 12 form the d-block, everyone here is a transition metal (blue). And the pier where we have docked, all the elements here belong to the f-block (cyan), on the bottom floor the actinides (beginning with Ac), and on the floor above them the lanthanides (beginning with La); many of them are radioactive.
+        <!-- Row 2 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">11 Gy</div>
+                <div class="col-title">Formation of Protocells</div>
+                <div class="col-toggle">
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+            <div class="t-content">
+                <div class="t-content-inner">
+                    As the early oceans became increasingly concentrated with complex organic molecules, these prebiotic compounds began to interact and organize into more sophisticated structures. Certain lipid-like molecules, driven by their hydrophobic and hydrophilic properties, naturally congregated in the watery environment to form spherical droplets with semi-permeable boundary membranes, often referred to as proteinoid microspheres or coacervates. These primitive structures, known as protocells, effectively isolated an internal chemical environment from the chaotic external surroundings. Within these enclosed micro-environments, organic molecules could concentrate, allowing for primitive metabolic reactions to occur at accelerated rates. Although these early protocells displayed remarkable lifelike behaviors—such as absorbing nutrients, growing in size, and even dividing into smaller droplets—they fundamentally lacked the true hereditary mechanisms necessary for Darwinian evolution. Nevertheless, the formation of protocells represented a critical evolutionary leap, bridging the gap between a disorganized chemical soup and the highly structured, compartmentalized architecture of the first true living cells.
+                </div>
+            </div>
+        </div>
-**Socrates:** Why exactly 118 rooms?
+        <!-- Row 3 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">11 Gy</div>
+                <div class="col-title">The "RNA World"</div>
+                <div class="col-toggle">
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+            <div class="t-content">
+                <div class="t-content-inner">
+                    Before the complex interplay of DNA and proteins became the standard operating system for all life on Earth, there existed a pivotal transitional phase known as the "RNA World." In modern biology, DNA stores genetic information, while proteins act as the molecular machines that catalyze chemical reactions. However, neither can function without the other, creating a paradox for the origins of life. Ribonucleic acid (RNA) offers an elegant solution to this chicken-and-egg problem. During this crucial epoch, RNA likely served a dual evolutionary role. It acted as both the primary carrier of hereditary genetic information and as an active catalyst—known as a ribozyme—capable of accelerating essential chemical reactions, including its own replication. This remarkable versatility allowed early RNA-based systems to undergo rudimentary forms of natural selection and evolution. The RNA World hypothesis elegantly bridges the profound gap between non-living chemistry and true biology, establishing the first self-replicating, evolving molecular networks.
+                </div>
+            </div>
+        </div>
-**Juno:** Because until now a total of 118 basic atoms have been discovered. Hydrogen’s atomic number is 1, oganesson’s is 118. In the nucleus at the center of an atom there are protons and neutrons, and around them are electrons. The number of protons in the nucleus is the atomic number. If there are as many electrons as protons, the atom is neutral; if there are more or fewer electrons than protons, ions are obtained: more means negative ion (since electrons are negative), fewer means positive ion. But the property of an atom is determined by the number of protons.
+        <!-- Row 4 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">11.5 Gy</div>
+                <div class="col-title">Emergence of Prokaryotes</div>
+                <div class="col-toggle">
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+                    Following millions of years of chemical evolution, the first undeniably living entities emerged in the dark, mineral-rich depths of the early oceans, likely clustered around hydrothermal vents. These pioneering organisms were prokaryotes—simple, single-celled life forms that entirely lacked a distinct, membrane-bound nucleus or complex internal organelles. Functioning primarily as anaerobic heterotrophs, these early bacteria survived in an oxygen-free environment by directly consuming the abundant organic molecules suspended in the primordial soup. Their simple but highly effective cellular architecture allowed them to thrive and rapidly reproduce in extreme conditions that would be lethal to modern life. The emergence of these resilient prokaryotes marked the definitive beginning of the Biological Age, as matter successfully crossed the threshold from complex chemistry to living biology. Over countless generations, these microscopic organisms dominated the planet, establishing the fundamental biochemical pathways that would eventually support the entire branching tree of life and transform the Earth's environment forever.
+                </div>
+            </div>
+        </div>
-**Socrates:** What do you mean by property of an atom?
+        <!-- Row 5 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">12 Gy</div>
+                <div class="col-title">Invention of Photosynthesis</div>
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+                    As the growing populations of early heterotrophic bacteria began to deplete the finite supply of free-floating organic molecules in the primordial oceans, an evolutionary pressure spurred a revolutionary biochemical innovation: photosynthesis. Certain innovative prokaryotes, most notably the ancestors of modern cyanobacteria, evolved the remarkable ability to harness the abundant, inexhaustible energy of sunlight. By utilizing solar radiation, these pioneering autotrophs could convert simple inorganic molecules—specifically carbon dioxide and water—into complex, energy-rich organic sugars, effectively generating their own food supply. This profound evolutionary leap liberated life from its dependency on scarce, naturally occurring chemical soup and allowed organisms to spread globally across the Earth's sunlit surface waters. The invention of photosynthesis not only secured an infinite energy source for the biosphere but also drastically altered the planet's atmospheric composition. By absorbing carbon dioxide and eventually releasing free oxygen as a metabolic byproduct, these microscopic solar engines permanently reshaped the trajectory of Earth's biological and ecological future.
+                </div>
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-**Juno:** You will understand with an example. Gold (Au, from the Latin Aurum) has 79 protons, and gold is such a solid that even at 1000 degrees Celsius it remains hard, to melt it requires 1064° Celsius. But by adding just one proton to it we get mercury (Hg), which melts and becomes liquid already at −40° Celsius, which is why at room temperature mercury is liquid inside a thermometer. That means just one proton can change the property of an atom so drastically.
+        <!-- Row 6 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">12.2 Gy</div>
+                <div class="col-title">The Oxygen Crisis</div>
+                <div class="col-toggle">
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+                    The proliferation of photosynthetic cyanobacteria initiated one of the most significant and catastrophic environmental transformations in planetary history, often referred to as the Oxygen Crisis or the Great Oxidation Event. For billions of years, life had evolved in an entirely anoxic environment, making the sudden accumulation of free oxygen—a highly reactive and toxic byproduct of photosynthesis—devastating to the established biosphere. As oxygen levels steadily rose in the atmosphere and dissolved into the oceans, it triggered a massive wave of extinctions among the dominant anaerobic organisms, for whom this new gas was a deadly poison. However, this profound ecological catastrophe simultaneously forged a new evolutionary frontier. Surviving organisms adapted to tolerate, and eventually harness, this volatile element. The integration of oxygen into cellular metabolism paved the way for aerobic respiration, a vastly more efficient method of energy production. This metabolic revolution ultimately unlocked the energetic potential required to support larger, more complex, and highly active life forms.
+                </div>
+            </div>
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-**Socrates:** I see. So the element Moscovium at number 115, does that mean it is found only in Moscow?
+        <!-- Row 7 -->
+        <div class="t-row">
+            <div class="t-header" onclick="toggleRow(this)">
+                <div class="col-time">12.5 Gy</div>
+                <div class="col-title">Eukaryotic Symbiosis</div>
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+                    The transition from simple, single-celled organisms to complex life was catalyzed by an extraordinary evolutionary event known as endosymbiosis. As the early oceans grew increasingly competitive, certain large, predatory prokaryotic cells began to engulf smaller, specialized bacteria. However, instead of digesting these consumed microbes for immediate energy, a mutually beneficial relationship formed. The engulfed aerobic bacteria, which were highly efficient at utilizing oxygen to generate energy, became permanent residents within the larger host cell, eventually evolving into modern mitochondria. Similarly, engulfed photosynthetic cyanobacteria were incorporated to become chloroplasts, the solar powerhouses of plant cells. This unprecedented biological merger created the first true eukaryotes—highly complex cells characterized by distinct, membrane-bound nuclei and specialized internal organelles. By combining the unique metabolic strengths of different organisms into a single, cohesive cellular unit, eukaryotic symbiosis provided the crucial structural and energetic foundation necessary for the subsequent evolution of all multicellular plants, fungi, and animals.
+                </div>
+            </div>
+        </div>
-**Juno:** You should cut down your annoying comedy, Socrates.
+    </div>
-**Socrates:** Leave aside judgment and give the answer.
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-**Juno:** Uranium’s nucleus has 92 protons, plutonium heavier than that has 94. Heavier than this are not found naturally in nature, scientists synthesized them artificially in the lab. In making Moscovium, Moscow’s scientists had the greatest contribution, that is why such a name.
+</body>
+</html>
-**Socrates:** Why are there no elements heavier than plutonium in nature?
+===== - Telescope =====
+{{https://upload.wikimedia.org/wikipedia/commons/thumb/9/92/The_Moon_and_the_Arc_of_the_Milky_Way01.jpg/1280px-The_Moon_and_the_Arc_of_the_Milky_Way01.jpg?nolink}}
-**Juno:** To understand that we need to go back to the story of the Particle Age. We heard from Ravi that if you bring two particles with the same charge very close, then stronger than their electromagnetic repulsion becomes the attraction of the strong force. That is why so many protons with positive charge can stay together in a nucleus. But if there are more than 94 protons, the nucleus cannot remain stable. That is why they are not in nature, they have to be made in the lab.
+The Atacama Large Millimeter/submillimeter Array (ALMA) serves as the definitive instrument for the Chemical Age, providing a high-resolution window into the molecular evolution of the cosmos. Located in the high-altitude Chajnantor Plateau of Chile, this interferometer consists of 66 high-precision antennas that work in concert to detect the faint radio signatures of cold gas and dust. While optical telescopes are blinded by the thick clouds surrounding infant star systems, ALMA’s submillimeter capabilities allow it to penetrate these "stellar nurseries" to map the distribution of complex organic molecules. By observing the rotational transitions of molecules in these environments, ALMA bridges the gap between simple atomic matter and the complex chemistry required for life.
-**Socrates:** Suppose we made them in the lab, but how did so many elements form naturally? In the Particle Age we saw that after the Big Bang the universe mainly produced hydrogen (76 percent) and helium (24 percent). Where did all the other elements come from?
+Technologically, ALMA’s power lies in its ability to detect the "spectral fingerprints" of a vast array of chemical compounds, including water, sugars, and amino acid precursors. The array functions by collecting millimeter-wave radiation, which is emitted by molecules as they rotate in space, and correlating the signals from dozens of antennas to create images with clarity surpassing even the Hubble Space Telescope. This allows researchers to observe the "snow lines" in protoplanetary disks—the specific regions where volatile compounds like water or carbon monoxide freeze onto dust grains. These observations are crucial for understanding the formation of oceans and atmospheres, as they reveal how the essential ingredients for habitability are distributed within developing solar systems.
-{{:bn:courses:ast100:starfurnace.webp?nolink|}}
+The legacy of ALMA in the Chemical Age is defined by its contribution to astrochemistry and our understanding of the prebiotic universe. It has successfully detected complex nitriles and alcohols in the interstellar medium, proving that the building blocks of life are not unique to Earth but are common throughout the galaxy. As the instrument continues to refine its observations of the periodic table in a cosmic context, it provides the necessary data to transition from the study of inanimate matter to the Biological Age. By identifying where and how complex molecules form, ALMA allows "citizens of the universe" to trace their own chemical heritage back to the cold, dark clouds of the early Milky Way.
-**Juno:** That is what is shown in this diagram, through a star 500 times bigger than the Sun. A few elements heavier than helium were produced in very small amounts right after the Big Bang, but almost all the elements of the periodic table were born inside stars. The first generation of stars were much more massive than the Sun, which is why they were able to produce many heavy elements. How that happens we heard in the Stellar Age.
-**Socrates:** Actually we did not hear. Mars said that in the cores of massive stars elements up to iron are created, but he did not explain well how.
-**Juno:** Then look again at the diagram above. You will see that in the final stage of life the core of a massive star looks like an onion, meaning it has many layers. At the very center is iron, outside it are several shells: first shell silicon, then successively magnesium, neon, oxygen, carbon, helium, and hydrogen shells. The star has built these shells of elements throughout its life. Let us hear again how. After all the hydrogen in the core has been converted into helium, nuclear fusion stops, and without outward pressure gravity compresses and heats the star. Then at one point the helium at the core’s center produces carbon, while outside remains a shell of helium. After all the helium in the core turns into carbon, fusion again stops, and as before the star compresses and heats up. As a result carbon in the core produces oxygen, outside remains a shell of carbon, and outside that still the previous helium shell. In this way, through the interplay of fusion and gravity, one layer after another is born. The heaviest element is at the center, the further out we go the lighter the elements we find.
-**Socrates:** On the right side of the diagram is it showing how long each reaction takes?
-**Juno:** It is showing how long each reaction continues in the womb of the star, and along with that the temperature required for each fusion reaction is shown in megakelvin and gigakelvin units. Hydrogen fusion that happens at 5 megakelvin lasts for 7 million years. But silicon fusion that happens at 2.5 gigakelvin takes place within just 1 day. That means the iron core of a massive star is made in just one day, this day can be called the last day of its life.
-**Socrates:** But iron has only 26 protons. Then where did all the elements from cobalt with 27 protons up to plutonium with 94 protons come from? The star, you said, has already reached the last day of its life.
-**Juno:** In the Stellar Age we heard that at death such massive stars explode as supernovae. At death through one enormous explosion the star gives us all the other elements as a gift. This is the star’s last donation to the universe. Let me explain how. Elements heavier than iron cannot be formed through normal fusion, because to make them requires investing more energy than is returned after they are made. Nature does not allow such losing reactions to happen. But during a supernova explosion suddenly such a vast amount of energy is released inside the star that it can be invested in reactions to make heavier elements. At the moment of explosion within only a few seconds many elements heavier than iron are born. But besides supernovae there are also some slower processes through which heavy elements can be made. We will not go into that detail.
-===== - Life on Earth =====
-**Socrates:** Excellent. Now while our boat is docked at this periodic table pier, I think you should tell us how life arose on Earth. We already heard about the origin of the oceans. Let’s assume that 4 billion years ago oceans were present on Earth. But how did all the elements from the womb of stars arrive inside those oceans?
-**Juno:** That you can already understand. After an explosion a star spreads all the elements inside it into the interstellar medium. The interstellar cloud from which our solar system was born already contained many elements because of the explosions and deaths of many neighboring stars. Since Earth was born from such a metal-rich cloud, it can be said that from the beginning it inherited all the elements.
-**Socrates:** Very well. Then tell us how from these inert elements we got biomolecules, microbes.
-{{:bn:courses:ast100:life.webp?nolink|}}
-**Juno:** Scientists do not yet know the whole process. But the most interesting hypothesis is shown in the diagram above. On the far left is a hydrothermal vent on the ocean floor. Scientists think that in such seafloor vents life first arose about 3.5 billion years ago. At that time the oceans were acidic, with a pH level of 6. Inside the ocean floor vents were alkaline or basic fluids, with a pH level of 11. In the acidic ocean there were positive hydrogen ions (H$^+$), meaning protons. In the alkaline vent there were negative hydroxyl ions (OH$^-$). Between the ocean and the vent there was a wall of iron–nickel sulfide, Fe(Ni)S, which created many microscopic chambers inside the wall. In these chambers, through the flow of protons coming down from the ocean water, from inert hydrogen and carbon dioxide the organic ion formate was created, with the formula HCOO$^-$. In this way, though not life, at least the organic was born from the inorganic.
-**Socrates:** Will it be enough just to make formate? Is life such a simple thing?
-**Juno:** Of course not. Formate is just one example. On the right side of the vent in the diagram the arrows above and below show the next steps. The first appearance of life actually took place through primitive metabolism, which is seen in the large cycle at the top.
-**Socrates:** I have heard of meatball, but I don’t know what metabol is, on top of that metabolism!
-**Juno:** I had wanted to explain, but after hearing your silly sarcasm the desire is gone. Ask your AI what metabolism is, not me. Let us return to the picture of proto-metabolism. You see a well-like structure resembling a cell, through whose wall protons (H$^+$) could enter, because the ocean outside the wall was positive and the inside was negative. With the flow of protons like a battery, possibly a primitive Krebs cycle was running inside this well, the biochemical cycle through which life obtains nutrients, meaning gathers energy from nutrients. Here the nutrients, meaning the inputs, were mainly hydrogen, hydroxyl, and carbon dioxide. And the outputs were four kinds of biomolecules most essential for life: lipids, sugars, amino acids, nucleotides. Life makes its cell walls from lipids, gets energy from sugars, makes proteins from amino acids, and makes RNA and DNA, that is, the genetic code, from nucleotides.
-**Socrates:** Is it the birth of all these things that is being shown next?
-**Juno:** Yes. Probably first protocells were made with walls of lipids, which floated in the stream of geochemical energy inside the vents. Inside these cells the very first thing needed is an information-processing system, or self-information. Without information the formation of life is not possible, it is not possible for thousands of bodies to replicate from one body. From nucleotides the first information system to arise was ribonucleic acid (RNA). The work of copy-paste was first begun by RNA. But the system became stronger when deoxyribonucleic acid (DNA) began to be produced. The work of coding information was taken over by DNA, RNA got the role of messenger. According to the code of DNA, various molecular machines, ribosomes and proteins, began to be made. With these the first living cell was formed. The first cells were not like human cells. Our eukaryotic cells are basically round, the primitive prokaryotic cells were elongated, and they did not have a nucleus. Thread-like DNA (shown in blue) floated in the fluid of the cell, not coiled in the center like our chromosomes.
-**Socrates:** Explain this genetic code thing. Processor, code, information, copy-paste — these are words we understand in the case of computer coding. What relation does a computer have with the cell of life?
-**Juno:** If you can once write down the perfect instructions for making something as a code, then with that code you can make that thing as many times as you wish, if the raw material is there. It was about 3.5 billion years ago that Earth first understood this on the chemical and biological scale. The alphabet in which computer code is written has only two letters, 0 and 1. With only these two letters an infinite number of “words” of different lengths can be made. In the cells of life the code is written with a four-letter alphabet, the four letters are the English A T C G.
-**Socrates:** What physically are A T C G?
-{{:bn:courses:ast100:dna.webp?nolink&800|}}
-**Juno:** A T C G are four nucleotide bases arranged one after another between the two helices of DNA, called nitrogenous bases because they are made with nitrogen. The diagram shows the DNA of our body. At the very top you see the two twisted helices. A base of one helix is bonded with a base of the other helix, two bases from the two helices together form a base pair (bp). Much like a spiral staircase: if the two railings of the staircase are the two helices, then the steps are the bases attached to the helices. On the left side you can see more clearly, the ribbon of the helix is made with phosphate and sugar, and inside them are set the bases. Bonds of A with T and C with G are shown. The structures of the ATCG bases are also given at the bottom left, you can see many carbons, nitrogens, oxygens, hydrogens. Three consecutive base pairs together form a codon, or triplet. Codons that come together to make a specific protein can be called a gene. From here the concept of the genetic code came.
-**Socrates:** Below the double helix I see many more things, with their sizes written.
-**Juno:** Yes, it is showing the packaging of DNA inside the cell. DNA base pairs (bp) of 2 nanometers (nm) in size are wound around histone proteins. 200 bp wrapped around a histone together make an 11 nm nucleosome, which in turn coils again into a 30 nm solenoid, each turn of which contains 6–8 nucleosomes. Many solenoid fibers together form 300 nm chromatin, which condenses into even thicker chromatids, 840 nm in diameter. Two chromatids joined with a bridge in the middle make one chromosome. Inside the nucleus of our cells there are 46 such chromosomes.
-**Socrates:** A gigantic tangle.
-**Juno:** In reality the tangle is even greater, I just simplified it.
-**Socrates:** Then to untangle it answer this question: through geochemical energy in this way, could the birth of life from the inorganic take place on any planet?
-===== - Habitable Zone =====
-**Mars:** Before that, we should set sail. We’ve seen enough of the periodic table. Just ahead the Teesta River meets the Jamuna.
-[From Shakhahati Ghat the boat departs; the eight arrive at the confluence of the Teesta and Jamuna.]
-**Socrates:** I’ve heard it was because of floods in the Teesta River that the Brahmaputra shifted from its old course through Mymensingh and came to join the Jamuna. Does anyone know?
-**Riya:** Yes, exactly 200 years before my birth, in 1787, a massive flood caused the Teesta to break into the Brahmaputra. From then on the Brahmaputra began its avulsion, shifting westward from its old eastern course. Over nearly fifty years it finally established the Jamuna as its main channel, while the old channel came to be called the Old Brahmaputra. On its banks the city of Mymensingh later built its park and the Zainul Abedin Museum.
-**Juno:** Looking from the boat at the vastness of the Teesta-Jamuna confluence, one truly feels why the Ganga-Brahmaputra Delta is called the most fertile place on Earth. For many thousands of years this region has been one of the most densely populated areas in the world.
-**Socrates:** Then tell me, could life exist on other planets too?
-{{:bn:courses:ast100:habitable-zone.webp?nolink|}}
-**Juno:** To understand that, first we must understand the concept of the habitable zone. Since galaxies, stars, and planets are all made of the same chemical elements, it can be assumed that life may emerge on many planets the same way it did on Earth. For life on Earth what was needed was oceans of liquid water. So, if a planet has oceans of liquid water, it may be habitable. In the diagram above you see the region around a star where, if a planet orbits, liquid water could exist on its surface—that region is called the habitable zone. Outside this zone, if a planet is closer to its star it will be so hot that water evaporates, and if farther away, the cold will freeze water into ice. Only inside the habitable zone does temperature remain between 0 and 100 degrees Celsius so that water stays liquid on the surface. However, for life the most favorable range is between 0 and 50 degrees.
-**Socrates:** In the diagram I see habitable zones for M, K, and G type stars. Why does the habitable zone shrink when the star’s temperature decreases?
-**Juno:** Just as in winter when the fire in your yard is weaker you need to sit closer to it for comfort, so too when a star’s temperature is lower, a planet must be closer to stay within 0–50 degrees Celsius. For a G-type star like the Sun, the habitable zone lies between 0.9 and 1.6 astronomical units (AU). The diagram shows that compared with G-types, M and K stars have two disadvantages: their habitable zones are smaller, and because they lie closer to the star, the amount of X-ray radiation there is higher, which is harmful for life. In fact, X-rays in the habitable zones of M-type stars are 400 times stronger than in those of G-types. Yet M and K stars have two advantages: they are far more numerous than G-types, and they live much longer. Since small stars endure for so long, planets orbiting them get far more time for life to evolve.
-**Socrates:** Does that mean that in the long run most living cultures in the universe may be found around smaller stars like M and K types?
-**Juno:** Possibly. It is also worth noting that our Mars was once within the habitable zone. About two billion years ago Mars had rivers and seas of liquid water on its surface, traces of which still remain. But whether life existed on Mars at that time is not yet known.
-**Socrates:** And what about exoplanets? How many planets have been found so far in the habitable zones of stars other than the Sun?
-{{https://upload.wikimedia.org/wikipedia/commons/thumb/f/fb/Diagram_of_habitable_zone_rocky_exoplanets%2C_from_NASA_Exoplanet_Archive_and_Gaia_DR3_data.png/1280px-Diagram_of_habitable_zone_rocky_exoplanets%2C_from_NASA_Exoplanet_Archive_and_Gaia_DR3_data.png?nolink}}
-**Juno:** Out of about 6,000 planets discovered so far, 70 have been found within their star’s habitable zone. Among these, about 40 planets resemble Earth most closely, and their names are shown in this figure. On the X-axis is the intensity of starlight on the planet’s surface relative to Earth, in percentage. Light intensity is directly related to the distance of the planet from its star. On the Y-axis is the star’s temperature relative to the Sun.
-**Socrates:** But how do scientists know for sure that these planets really are in their star’s habitable zones?
-**Juno:** From a star’s brightness and distance its temperature can be calculated, and from the temperature the habitable zone can be determined. When exoplanets are discovered using the transit method, the planet’s distance from the star is also known, because its orbital period depends on that distance. Once you know the distance, you can tell whether the planet is in the habitable zone.
-**Socrates:** But just being in the habitable zone doesn’t guarantee life. And even if there is life, how can we ever detect it?
-===== - Searching for Life =====
-**Juno:** To search for life on a planet, first we must detect its atmosphere. If certain molecules are present in the atmosphere, then we can assume life may exist there. These molecules are called biosignatures. For example, without O$_2$ and O$_3$ in Earth’s atmosphere, advanced life like ours could not exist. Besides these two, water vapor, methane, nitrous oxide, and methyl chloride are also considered biosignatures. Six years ago, in 2019, water vapor was detected in the atmosphere of K2-18b, an Earth-like planet within the habitable zone.
-**Socrates:** And how are biosignatures in an atmosphere detected?
-{{:bn:courses:ast100:spectra.webp?nolink|}}
-**Juno:** They are detected through spectroscopy, that is, by analyzing a star’s light into different colors. The chart of how much light comes at which color (wavelength or frequency) is called a spectrum. This figure shows three kinds of spectra: continuous, emission, and absorption. If you directly analyze the light of a star, you get a continuous spectrum, because a star radiates light at all wavelengths. In contrast, light from a gas cloud comes only at certain wavelengths, so its spectrum is an emission spectrum. To understand the difference, recall the Particle Age: light is produced due to the acceleration of electrons. Inside a star’s high temperature, countless free electrons move with all possible accelerations, producing light of all frequencies. But in a gas cloud, where the temperature is lower, there are no free electrons. Light there is produced only through the transitions of bound electrons inside atoms—that is, when electrons jump from one energy level to another. Each transition produces light of a unique wavelength, depending on what kinds of atoms and molecules are present. Thus, from an emission spectrum we can know the chemical composition of a gas cloud.
-**Socrates:** And the absorption spectrum?
-**Juno:** That is the most important. If a star’s light passes through a gas cloud before reaching us, then that cloud absorbs light at exactly those wavelengths it would have emitted. So in the star’s spectrum, light is missing at those precise wavelengths, appearing as dark lines in the chart. These are called absorption lines. Physicists have already identified which molecule produces which absorption line. By matching a star’s absorption spectrum with laboratory spectra, we can know which molecule is responsible for which line.
-**Socrates:** I see. But where exactly is the gas cloud that the star’s light passes through? And how does that connect with discovering a planet’s atmosphere?
-{{:bn:courses:ast100:transmission-spectra.webp?nolink|}}
-**Juno:** Since we’re close to the Padma, let’s not drag this out. I hope you’ve guessed already where the gas cloud is. Still, let me show you in the figure above. During a transit, when a planet passes in front of its parent star along our line of sight, the star’s light dims slightly. But part of that light must then pass through the planet’s atmosphere before reaching us. The gas cloud mentioned earlier is this very atmosphere. That means the absorption lines we see in the star’s spectrum are actually imprints of the molecules in the planet’s atmosphere. The star’s spectrum thus becomes the fingerprint of the planet’s atmosphere. Such spectra are called transmission spectra.
-**Socrates:** Wonderful. It seems nature itself is eager to reveal its secrets to us.
-**Juno:** I sometimes feel the same. By now, atmospheres of many planets have been detected, but no Earth-like planet’s atmosphere has yet shown all biosignatures. If found, its spectrum would look like what you see in the figure above—from oxygen and ozone lines near 0.3 microns all the way to carbon dioxide lines at 16 microns in the infrared. Notice the lines are broad, not narrow. Because of molecular motion and the Doppler shifts associated with it, every absorption line broadens. In the transmission spectrum of an Earth-like planet, you would also see water and methane. Unless all of these are found together, we cannot give definitive proof of life on any planet.
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