01-birth.Rmd

# The Birth of the Universe

>In the beginning the Universe was created. This has made a lot of people very angry and been widely regarded as a bad move.  
_Douglas Adams, The Restaurant at the End of the Universe_

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A classic question in philosophy is as follows: Why is there something rather than nothing? Which is to say, why is there a universe, and why is it full of stuff? Wouldn't it be just as easy---maybe easier!---for there to be simply nothing at all? What even is the universe? How did it originate? _When_ did it originate? How did it develop? Common wisdom tells us that the universe is constantly expanding---but into _what_ is it expanding? And why do we care? 

Why we care is a complicated question with no singular answer, but I think we ought to care because life exists today as we know it because of the events that birthed and shaped the universe. Understanding life requires that we understand the physical laws that govern its construction. In fact, all of us here on Earth are really products of just one event that occurred nearly 14 billion years ago. In all the time and space of the universe, we only know of a single planet capable of supporting complex biological life. Our singular example suggests that a lot of very specific things were necessary for the formation of life, and that the life we know is irrevocably tied to the planet on which it formed.

## 1: The Big Bang {-}

Let's start with the what. The **universe** is all of space and time and all matter and energy contained within it. Us humans usually care most about the planets, galaxies, stars, nebulae, and comets---because that's the stuff we can see. But this matter---which we call **ordinary matter**---actually represents only five percent of the matter contained in the universe. We know the most about this kind of matter, because, well, we can see it, and touch it, and also we _are_ it. Yet nearly 24 percent of the matter and 71 percent of the energy in the universe is invisible to the entire electromagnetic spectrum, including all of human visible light. We call this **dark matter** and **dark energy**, because, well, we can't see it, we can't touch it, and we decidedly are _not_ it. We're not even exactly sure what it is although we do know it's there.[^3]


![M81 spiral galaxy image from [NASA](https://images.nasa.gov/details-PIA09337), an example of "ordinary matter."](images/galaxies.jpg){width="60%"}


We have a few good ideas about the birth of the universe and its age, and we call these ideas the **Big Bang Theory**. In regular speech, we might use the word theory to mean that we have a half-baked idea---_I have a theory that my television is brainwashing me with special light pulses._ But a **scientific theory** is something very different. It's usually a principle that has been tested repeatedly from many angles, over many years, often centuries. It's something that we can use to make accurate predictions about the future behavior of specific phenomena. Here is a comprehensive definition from [Wikipedia](https://en.wikipedia.org/wiki/Scientific_theory):

>A scientific theory is an **explanation** of an aspect of the natural world and universe that has been **repeatedly tested** and **corroborated** in accordance with the scientific method, using accepted protocols of observation, measurement, and evaluation of results. Where possible, theories are tested under controlled conditions in an experiment. In circumstances not amenable to experimental testing, theories are evaluated through principles of abductive reasoning. **Established scientific theories have withstood rigorous scrutiny and embody scientific knowledge.**

Here are just a few scientific theories you may have heard about: [The Theory of Gravity](https://en.wikipedia.org/wiki/Gravity), [The Theory of Relativity](https://en.wikipedia.org/wiki/Theory_of_relativity), [The Theory of Evolution By Natural Selection](https://en.wikipedia.org/wiki/Evolution_by_natural_selection), and [The Laws of Thermodynamics](https://en.wikipedia.org/wiki/Laws_of_thermodynamics). But let's get back to the theory of the day, the Big Bang.

### The uncertainty in the beginning {-}

My favorite part about the Big Bang Theory is that the "big bang" didn't start out big at all, and there was no bang. (There is no sound in space.) For those reasons, I've read that cosmologists actually hate the term "big bang," but unfortunately for them it's super catchy so it stuck. Over the thousands of years of recorded human history, human beings have put forth countless stories---creation stories---that attempt to explain the birth of the universe. I'm partial to the Finnish diving duck, whose egg fragments on the knee of the goddess of air gave birth to the world. 

The goal of science is to systematically test explanations and predictions in an effort to build and organize human knowledge. This goal is sometimes analogous to our goals in storytelling and sometimes not. In the case of creation stories, I think the goal is the same---we want to know where we came from and why we are here. We search for meaning in the fact of our existence. But despite the decades of research there is still a lot of uncertainty surrounding the birth of the universe. The fact is, we still are not entirely sure _where_ the universe came from or _why_ it was suddenly there.

Part of the problem is that the universe is said to have started with a **singularity**. A singularity happens when gravity is so intense that all known physical laws of space and time completely break down. In our universe, predictable physical laws governing space and time (or, "spacetime") allow us to understand the behavior of matter and energy. But when these laws break down we have no language for that---what is "time," before time existed? And really, who's to say that a singularity isn't just a fancy name for a great cosmic egg? Because it is this singularity that gives birth to the universe.

All we know is that at some instance all the matter and energy that would ever be _in the entire universe_ was condensed into a single point: the singularity. The conditions of this single point are so extreme that physical laws break down, so it's impossible to say what occurred during the earliest moments of the Big Bang. The temperature is so high in the early stages of the universe that atoms, the stuff that makes up all ordinary matter, cannot form. The four fundamental forces that govern everything in the universe---gravitation, electromagnetism, the weak nuclear force, and the strong nuclear force---did not exist at all as separate forces but were unified as one.

![The universe begins with a singularity. (Photo from [Wikipedia](https://en.wikipedia.org/wiki/Cosmogony#/media/File:Universe_expansion-en.svg).)](images/expansion.jpg){width=40%}

But from this singularity the universe begins to expand.

### Inflation and the four fundamental forces {-}

As the universe expands, it cools. Between 10^−36^ seconds and 10^−32^ seconds after the singularity begins to expand, this single unified force governing all interaction begins to split into two forces that will eventually become four. But first. An event occurs that should be impossible based on everything we know about science and the universe: in barely a fraction of a second, the universe expands from roughly the size of a three-story building to something 62,100,000,000,000,000 miles across. This event is known as **inflation**.

In our knowable universe, nothing can travel faster than the speed of light. Rather than suggesting that the universe expanded faster than the speed of light, scientists say that the metric that governs the geometry of spacetime changed in scale. Basically, and I'm no physicist, the entire scale of the universe changed, like zooming in really close on a picture. The picture itself did not change but the scale did. 

Through this expansion, the universe can continue to cool. The entire universe is completely filled **quark-gluon plasma**, a hot, dense collection of particles that will ultimately condense to form matter but hasn't yet. The universe is still too hot for that. But those four fundamental forces that constrain the behavior of all matter in the universe---gravity, electromagnetism, and the strong and weak nuclear force---now exist in the form we know them today.

```{r, fig.cap="A description of the four fundamental forces. These four types of interactions are not reducible to more basic interactions."}
library(tidyverse)
col1 <- enframe(c("Gravity",
                  "Electromagnetism",
                  "Strong Nuclear Force",
                  "Weak Nuclear Force",
                  "Electroweak Force"), name = NULL, value = "Forces")

col2 <- enframe(c("All things with mass or energy are attracted to (or gravitate toward) one another.",
                  "A type of physical interaction that occurs between electrically charged particles, carried by electromagnetic fields composed of electric fields and magnetic fields.",
                  "An interaction that keeps the particles that make protons and neutrons together, and binds protons and neutrons into atomic nuclei.",
                  "An interaction between the components of atoms that is responsible for the decay of atoms.",
                  "At extremely high temperatures, the electromagnetic force and weak force merge into a combined electroweak force."), 
                name = NULL, value = "Description")

table <- cbind(col1, col2) 

knitr::kable(
  table, booktabs = TRUE, caption = "A description of the four fundamental forces. These four types of interactions are not reducible to more basic interactions."
) %>%
  kableExtra::kable_styling(bootstrap_options = 
                              c("striped", "hover", "condensed", "responsive")) %>%
   kableExtra::column_spec(1, bold = T, border_right = T, width = "10em") %>%
   kableExtra::column_spec(2, width = "30em")

```

### Matter and antimatter {-}

It's actually not clear why there is any matter in the universe at all. In the hot mess of the early universe, both matter particles and antimatter particles are created together in pairs. These are similar particles but with opposite charges, and when they come into contact they destroy ("annihilate") each other. Because they are created in pairs, that means that ultimately every matter particle should eventually destroy every antimatter particle and there would be nothing left except pure energy. But this is not a universe of pure energy. For all the "stuff" we see in the universe, from every nebula to every comet, from every planet in our solar system to every human-made artifact on Earth: _something_ is there. Something is there because for every billion pairs of matter and antimatter created in the early universe, two matter particles were not annihilated. Two matter particles remained.

And we are the remnants of that great cosmic imbalance.

![So far, we have discussed the first second of the history of the universe following the Big Bang. (Photo from [Wikipedia](https://en.wikipedia.org/wiki/Chronology_of_the_universe#/media/File:CMB_Timeline300_no_WMAP.jpg).)](images/bigbang.jpg){width=80%}


## 2: The Formation of Matter {-}

I've spent a lot of time talking about mass, and atoms, and parts of atoms. But what actually is all that stuff? When we hold something in our hands, what is it that we are holding? Pinch your skin---something is there... but what? It's ordinary matter, which is simply anything that takes up space and has **mass**[^1]. But wait, you say, skin is mostly made up of proteins. That's true. But what makes up proteins? Maybe you already know that proteins are made of amino acids. Okay, what makes up an amino acid? Mostly carbon, nitrogen, oxygen, hydrogen. Now we're getting somewhere. But what makes up carbon? Oxygen? Nitrogen?

Recall that at some point very soon after the Big Bang, the entire universe is filled with a substance we called "quark-gluon plasma." We will get into the states in which ordinary matter can exist (solid, liquid, gas, and plasma), but first let's talk about quarks and gluons. A **quark**[^2] is one type of **elementary particle**, or, in other words, a particle that is not composed of any other particles---it is irreducible. A **gluon** is another kind of elementary particle. You don't need to know about their properties, just that they are two important elementary particles.

![Mmm, let's construct a pie from scratch. Starting with an atom.](images/pie.png){width=45%}


Why are the starting ingredients quarks and gluons? Because we want to build an **atom** from scratch, like a delicious apple pie. All ordinary matter is made up of different types of atoms that we call **elements**---we know about 116 of them which you can find on the periodic table. An atom is essentially the smallest bit of an element that you can get while still retaining the "special properties" of that particular element. What are the "special properties" of an element? What makes "oxygen" so "specially oxygen"? We'll get to that, but we'll start first with how atoms were built. Because there was a time when there weren't any atoms at all!

### Making the atomic nucleus {-}

Okay, so let's return to the early universe. The _very_ early universe. A whole second hasn't even passed yet. Energy is too high for any meaningful interaction between quarks and gluons; it's just too dang hot. Hence the plasma. But as the universe continues to expand and cool, quarks can now interact with gluons. When quarks and gluons are finally able to bind together, they create something called a **hadron**---there are a few kinds of hadrons, but the ones will focus on are called **protons** and **neutrons**. These particles are important because they will ultimately make up most of the ordinary matter in the universe as they bind together and form an **atomic nucleus**. Protons have a positive charge and neutrons have a neutral charge.

![A depiction of a proton, a positively charged subatomic particle, made up of three quarks and the gluons that mediate their interaction. The strong nuclear force holds these particles together. (Diagram from [Wikipedia](https://en.wikipedia.org/wiki/Quark#/media/File:Quark_structure_proton.svg).)](images/proton.png){width=30%}

Between 10-20 seconds following the Big Bang, protons and neutrons are finally able to bind together. We call protons and neutrons **subatomic particles**, because they are two of the three main components of an atom. Now, the first element on the periodic table is one that we call hydrogen. Hydrogen is first on the periodic table and it has a little "1" next to it, which is its **atomic number**. The atomic number tells us how many protons an element contains, so in this case, one proton. We know that protons are positively charged, and the very first elements created in the universe were made up of only protons and neutrons: hence, they were positively charged. When an element has a charge we call it an **ion**. Positively charged hydrogen ions dominated the early universe, and even today, hydrogen makes up 75% of all ordinary matter _in the whole universe_.

![The element hydrogen on the periodic table. Hydrogen's atomic number is one, meaning it has one proton.](images/hydrogen.png){width=23%}

### Making the whole atom {-}

In the early universe, we form a few elements with only protons and neutrons. These are ions because they are all positively charged, including helium-4 (two protons and two neutrons), and lithium-7 (three protons and four neutrons). But for the next 370,000 years, the universe is still too hot and too dense to form a bona-fide atom. Which is to say we have no "neutral" elements; every element has a positive charge. What are we missing to make a real atom? We're missing something called an **electron**. Electrons are the third subatomic particle: they are tiny as hell and they are negatively charged. The reason why all the elements on the periodic table are depicted without a charge (neutral) is because they have the same number of electrons as protons, so neutral hydrogen has one electron and one proton. But the universe still needs to cool for this to happen.

Finally, sometime about 300,000-400,000 years after the Big Bang, we see a period called "Recombination." Finally, electrons bind with protons and neutrons and we form the first neutral atoms.

![The element helium, which contains two protons and two neutrons in the atomic nucleus, also held together by the strong nuclear force. Surrounding the atomic nucleus is an "electron cloud" with two electrons.](images/helium-atom.jpg){width=45%}

### Making more elements {-}

Hydrogen, helium, and a smattering of lithium are formed as the universe continues to cool. For millions of years, the universe is simply dark. There are few photons and no stars. And there are no elements heavier than lithium in the universe. You see, to make an element heavier than lithium requires something called **nuclear fusion**. Basically, if we "fuse" the atomic nuclei of two helium elements, we can make beryllium---we added two protons and two neutrons to make an element with four protons and four neutrons. But this process requires wicked force.

There is only one thing that we know of that carries out the process of fusion naturally, and that is stars. Our sun is a star, and it's constantly fusing hydrogen atoms to make helium, which lets off such explosive force that it holds the entire solar system in place and powers the existence of all life that has ever been on Earth. In fact, the sun accounts for 99.86 percent of the total mass of the entire Solar System: so you, and me, and everything and everyone we know, and all the crap we made on Earth, and Earth, and all the other planets, and comets, and meteors, all that stuff is just the 0.14 percent matter leftovers.

![Positively charged atomic nuclei repel each other, and it takes a lot to overcome the energy barrier of these forces. (Image from [Wikipedia](https://en.wikipedia.org/wiki/Nuclear_fusion#/media/File:Nuclear_fusion_forces_diagram.svg).)](images/nuclear-force.png){width=60%}


Eventually, all stars exhaust their supply of hydrogen.[^4] Depending on the size of the star, things can start to get crazy. We will focus on stars whose mass is very large (not our sun, which is comparatively smaller). Once hydrogen supply is exhausted the star will start fusing other stuff, like helium to make beryllium, beryllium to make oxygen, and so forth. Stars can use atomic nuclei to power fusion all the way up until the element iron (26 on the periodic table).

![A supernova in the M82 galaxy. (Image from [NASA](https://www.nasa.gov/chandra/multimedia/supernova-sn2014j.html).)](images/supernova.jpg){width=55%}

One of the awesome things about fusion is that it helps maintain a star's shape and size by providing a constant outward pressure that exists in tandem with the inward gravitational pull exerted by the star's mass. Remember, stars are very, very, very large. This perfect balance exists until fusion starts to slow. As fusion slows, the outer pressure exerted by it abates, and now the core begins to condense. Eventually as a last gasp the star attempts fusion with iron. (Whoa, buddy!) Repulsion of iron atoms' nuclei crushed closely together would create an implosion as the star collapses under it’s own weight---but instead neutrons halt the implosion, matter bounces off the hard iron core, and BOOOOOOOM! A gigantic, superhot shockwave catapults its way through the cosmos jettisoning matter at 9000-250000 miles per second.


Why do we care about this? We care because the fusion reactions in stars cannot create anything heavier than iron. That means the heavier elements---especially the metallic ones that make up, say, a terrestrial planet like Earth---only come from these explosions. And in their wake, they leave nurseries where new stars may form, different stars made of different kinds of elements, and planets may form from the leftovers that surround them.


![The Crab Nebula is the result of a supernova that occurred in 1084 A.D. that was documented by humans. (Image from [NASA](https://www.nasa.gov/multimedia/imagegallery/image_feature_1604.html).)](images/crab.jpg){width=60%}


### Combining elements together {-}

Protons are what determines what an element is---if you change the number of protons, you change the element. But you can change the number of neutrons or electrons and the element stays the same. If we have an atom of helium with two protons, two electrons, and two neutrons, it's neutral. But we can change the number of electrons and it will become a positively or negatively charged ion. Or, we can change the number of neutrons, and it becomes an **isotope**. So we would say that the proton is what determines the element's identity.


![An electron distribution diagram for the element nitorgen. The first shell contains two electrons and the second shell contains five electrons. But the second shell can hold eight!](images/nitrogen.png){width=23%}


But the electron is what determines it's chemistry. The reason is that when elements bind together to form **molecules**, it's the electrons that are doing the binding part. Surrounding the atomic nucleus are **electron orbitals** that contain specific numbers of electrons. The first **shell** contains two electrons, and the next shells all contain eight. But take the element nitrogen: it has seven electrons, and we would depict it in a diagram above.

But we know that every shell after the first shell can hold _eight_ electrons, and there are only five here. Nitrogen is not very happy like this. Atoms are most stable when their orbitals are filled. So what's a lonely nitrogen to do? Well, it can _share_ electrons with another atom, called a **covalent bond**. Nitrogen is happy when it's triple-bonded to itself in the form of N~2~. But, it can also bind with three hydrogen atoms and form NH~3~. 


![Nitrogen has greater electronegativity than hydrogen, so it pulls electrons closer to itself. This gives nitrogen a slightly negative charge and hydrogen a slightly positive charge.](images/electronegativity.jpg){width=40%}


Some atoms pull electrons toward themselves more than other atoms, a property called **electronegativity**. If one atom is more electronegative than another atom, it will pull the electrons they share closer and have a slightly negative charge. This is called **polarity**, and it will soon become very important.

## 3: Our Pale Blue Dot {-}

The Milky Way Galaxy is old. Very, very old. Its estimated age makes it among the first galaxies to form 13 billion years ago. How did galaxies even form? The leading hypothesis is that tiny quantum fluctuations[^5] that existed when the universe inflated created unevenness in the resulting distribution of matter in the universe. These pockets of matter will eventually form **galaxies**, which are a group of stars, planets, stellar remnants, gas, dust, and dark matter that are gravitationally bound to one another. As galaxies grow in size, pockets of hydrogen may form that will ultimately collapse and form a **protostar**, a very young star that is still accumulating mass. It can take up to half a billion years for fusion to begin in the star's core and the protostar to become an actual star. A star typically has such a high mass that its gravitational pull on surrounding objects is very large.


![The Milky Way Galaxy is nearly 200,000 light years across, so we are not totally sure of its shape. But we think it looks like this galaxy, UGC 12158. If the solar system were the size of a quarter, the Milky Way would be the size of the United States (Image from [Wikipedia](https://en.wikipedia.org/wiki/Milky_Way#/media/File:UGC_12158.jpg).)](images/UGC_12158.jpg){width=55%}


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### The birth of the solar system {-}

Several billion years after the Milky Way forms, about four and a half billion years ago, a large pocket of hydrogen gas, more than 25,000 light-years from galactic center, begins to collapse. Because only giant and short-lived stars produce the supernovic explosions we learned about previously, we know that the sun probably formed in a region where massive stars form and ultimately explode. We know that the sun formed from the remnants of an earlier star, because the elements contained within the solar system could not have existed without a supernova creating them. 

The sun, like other stars, emerges when the outward pressure exerted by the gas pocket is overwhelmed by the inward pressure of gravity and a protostar is produced. Around this protostar a disk of particles starts to spin and condense, and the atoms contained within it collide with greater and greater frequency. This makes things very hot. But it takes about 50 million years for the sun to transform from a protostar to a **main sequence star**, where it is stable and powered by nuclear fusion at its core.


![A star-forming region, the Sharpless 2-106 Nebula, captured by the Hubble Space Telescope. (Image from [Wikipedia](https://en.wikipedia.org/wiki/File:Star-forming_region_S106_captured_by_the_Hubble_Space_Telescope.jpg).)](images/star-formation.jpg){width=75%}


The sun is born in a stellar nursery called a **nebula**. Its thought that many stars formed in the nebula that birthed the sun, and that the sun eventually migrated away from its hometown, so to speak, away from the other stars that were born there. Because the sun is so massive---we already know that most of the mass in the solar system is contained within the sun---its gravity strongly influences the surrounding matter. This is important because as material starts to spin around the sun in orbit, due to its mass, this material may eventually form planetary bodies.


![The sun is so massive that it essentially causes a dip in the fabric of spacetime that other objects can orbit. I imagine this like these coin donation games where the coins spin around the center.](images/coinspin.jpg){width=55%}



### The formation of planets {-}

Not all galaxies are capable of supporting complex biological life. The formation of a terrestrial planet of a suitable size in a suitable location---away from gamma ray bursts, globular clusters, frequent supernovae, and Oort cloud comets, among other things---appears to depend primarily on the location and composition of the sun around which the planet forms. Which is to say that the pocket of interstellar dust that formed our solar system determined---long before our sun ever existed---whether or not a terrestrial planet could form at all. We need metallic elements for that.


![We are still trying to figure out what a planet is, so sometimes Pluto is included and sometimes Pluto is excluded.](images/plutomeme.jpg){width=35%}


Let's try and first figure out what a planet even is---you may have heard a lot of debates about Pluto in the last decade or so. _It's a planet; it's not a planet; wait, it is a planet!_ Nothing has changed about Pluto. The reason for the debates is that we have not actually settled on a definition of the word "planet." So really we are having debates about language. Part of the problem is that if we use a definition that includes Pluto, then there are actually _way_ more than nine planets in the solar system. There are hundreds. It's just that when we first defined the word we didn't know that.

We will use the definition of **planet** as defined by the International Astronomical Union (IAU):

>a planet is a non-stellar body that is massive enough to be rounded by its own gravity, that directly orbits a star, and that has cleared its orbital zone of competing objects.

Planets typically form through a process known as **accretion**. When the protostar is born all the particles of gas that spin around it start smashing up against each other and sticking. This forms larger and larger objects over time. The planet that is produced depends on what sticks together during this process---meaning, the kinds of elements that are contained within it. A **terrestrial planet**, which is what Earth is, is made of silicate rocks and metals. Jupiter is a gas giant that contains only a liquid hydrogen core and hydrogen gas.

The terrestrial planets of the inner solar system---Mercury, Venus, Earth, and Mars---formed there because it was too hot for gas giants or ice planets to form. Only metal could withstand the blazing heat of the sun. (It is no coincidence that Mercury is made of solid iron.) Metallic elements are actually rare in the universe which is why these planets do not get very large. Beyond the **frost line**, the solar system becomes cool enough that giant planets like jupiter, saturn, uranus, and neptune can form. These planets grew large because they captured most of the hydrogen and helium not taken up by the planets of the inner solar system.

### Earth is formed {-}

At some point, the inner solar system contains 50-100 protoplanets that are the size of Mars or smaller. These continue to smash into each other and coalesce to form larger bodies. From the chaos of all this smashing comes our home planet of Earth, the only known astronomical object that contains life.


![The Giant-Impact Hypothesis suggests that the moon was formed when proto-Earth collided with a planetary object the size of Mars. Analysis of lunar rocks suggests that both bodies were thoroughly mixed upon impact. (Image from [Wikipedia](https://en.wikipedia.org/wiki/Giant-impact_hypothesis#/media/File:Artist's_concept_of_collision_at_HD_172555.jpg).)](images/moon.jpg){width=65%}



But first. Early in its life, Earth is not stable: fluctuations in its rotation would eventually cause severe seasonal extremes problematic for imminent life. While some organisms may adapt to extreme variations in temperature, many could not. Around when the rocks that comprise the Earth were mostly accumulated and molten, as they traveled in orbit around the sun, a collision occurred by chance with a planetary body that was roughly the size of Mars. The remnants of this collision stabilize the Earth's rotation and can still be seen today with the naked eye. We call it the moon.

The Earth is composed primarily of four layers. Once Earth was mostly formed, melting caused denser substances to sink toward the center while materials with less density migrate to the top. This process is called **planetary differentiation**. 


![The layers of Earth. (Image from [Wikipedia](https://en.wikipedia.org/wiki/Earth#/media/File:Earth_cutaway_schematic-en.svg).)](images/earthcore.png){width=65%}


1. Let's start at the **inner core**: we think it's composed of an iron-nickel alloy, based on analysis of the Earth's magnetic field. Essentially, without this, we could not have a magnetic field at all. The magnetic field is important for life, because it diverts high-energy particles from the sun and dramatically reduces the radiation impact on Earth. The core is also very hot, about 10,000 degrees F. (This is approximately the temperature on the surface of the sun.) We have never directly measured the Earth's core, which is four thousand miles below the surface.

2. Next is the **outer core**, which is also iron-nickel, but instead of being solid it is liquid. The outer core is about 1,800 miles below the surface.

3. The **mantle** is the thickest layer, and movement in the mantle is responsible for things like earthquakes and volcanoes. It is also responsible for the motion of tectonic plates in the earth's crust, causing the formation of mountain ranges, among other things.

4. The **crust** is the outermost layer of the Earth and the one we live on.

Right now, on early Earth, right after the giant impact, the scene is very, very bad for biological life. The entire planet is thought to be molten lava to a depth of hundreds of kilometers or more. There is no stable atmosphere, no liquid water, no solid crust, and no magnetic field. These components are all necessary for prebiotic chemistry to occur that is needed for the emergence of biological life.

## 4: The Scene on Early Earth {-}

Water is so important to every aspect of life on Earth that many hypothesize that life without water---on any planet---is not possible. Cells, the basic building block of life, are mostly made of water. Many chemical reactions carried out by living organisms depend on the presence of water. Earth's surface is about two-thirds water and so are we. But more than these examples, the very construction of water---and all the special properties that emerge from that construction---mean that water shapes and influences almost every aspect of the business of life. It's important enough that we'll focus our exploration of early Earth on the origin and maintenance of water on the planet.

But I'm getting ahead of myself. How do we actually know the age of the Earth? We use a special property of atoms that relates to the weak nuclear force. Remember that an atom is made up of positively charged protons and neutral neutrons, surrounded by a negative electron cloud. The mass of a particular atom is primarily composed of the neutrons and protons, because the electrons are very, very, very, very light. Now, we can't change the number of protons of an atom without changing what element it is---but we _can_ change the number of neutrons and the element stays the same.

![When no time has passed (zero half-lives) the atoms are all that of the parent isotope. As it decays over time, the parent isotope decays to the daughter product. There are different kinds of decay that we will not cover in class: you just need to know that the rate of decay is constant and can be measured. ([Image source](https://courses.lumenlearning.com/cuny-lehman-geo/chapter/radiometric-dating-methods/).)](images/half-lives.jpg){width=75%}


You may have heard of something called **carbon dating**. On the periodic table, you'll see that carbon has an atomic number of 6; it has six protons and also six electrons (in its neutral form). Its **atomic weight** is 12, which is the number of protons plus the number of neutrons. This means that typically carbon has six neutrons. But there's another form of carbon, an isotope called ^14^C that has two additional neutrons. Carbon-14 is actually radioactive, and it isn't stable. Thus over time it decays. The rate that it decays can be measured, and scientists use a constant called its **half-life**---the time required for the quantity to reduce by half---to date an object. The half-life of ^14^C is 5730 years.

It's not just carbon; this can be done with other kinds of isotopes, too. We call this **radiometric dating**. Different isotopes will have a different half-life---^3^H is ten years, and ^147^Sm is 100 billion years. Depending on the timescale of interest and the isotopes available to measure, scientists can use this radioactive decay to learn the age of rocks, fossils, and even our home planet.

Getting back to the point: using radiometric dating, we can infer the age of the Earth. We can't actually use the rocks themselves, because conditions on early Earth were so chaotic that these early rocks have been recycled and destroyed over time. The oldest actual rock-rocks on Earth are roughly four billion years old, and several have been found across the planet ranging from 3.3-3.8 billion years old. Scientists have used several different isotopes to measure the ages of these rocks with consistent results. Radiometric dating from moon rocks provides ages of the oldest rocks at 4.4-4.5 billion years old. Since the moon was formed by a blast to very early Earth, this also helps us narrow down our planet's age. The oldest recorded material found on Earth are grains of zircon (crystals) found in Western Australia, roughly 4.1 billion years old.

### Plate tectonics {-}

You may be wondering what I mean when I say the rocks on Earth have been recycled. The surface of the Earth, the crust, is not static, which is to say that it's moving all the time. Not a lot, but a little bit (about 1-3 cm per year). Why does the crust move? Because right under the crust of Earth is magma, which is essentially liquid rock. But below that is the core, which is basically as hot as the surface of the sun. That's a lot of pent up heat---you can think about when you boil a pot with the lid on top, and the lid starts shaking as the water gets hot. The other important thing to know is that the crust of the Earth is not just one solid piece, but it's made up of many pieces---**plates**---kind of like the fabric around a baseball. Essentially what happens is that the heat from the core rises up, as it rises it cools, and then it sinks down again---this process is what fuels the shifting of the Earth's crust, known as **plate tectonics**.

![The red dots are earthquakes of a magntiude greater than seven; the yellow triangles are active volcanoes. This is the Ring of Fire, a continuous series of subduction zones where rock is constantly recycled. Volcanoes are created and earthquakes are common. (Image from [Wikipedia](https://en.wikipedia.org/wiki/Ring_of_Fire#/media/File:EQs_1900-2013_worldseis.png).)](images/ring.png){width="70%"}

The plates that make up the Earth's crust have different kinds of boundaries---convergent ones, where the plates are being pushed together, and divergent ones, where the plates are being pulled apart. This results in all kinds of things, like earthquakes, volcanoes, mountain ranges, and deep ocean trenches. (California is located within the **ring of fire**, an enormous area where rock is continuously being recycled.)
 
We do know that after the formation of the atmosphere, liquid water ultimately condenses on the surface of Earth, creating the oceans. The Earth was really hot, probably close to 500 degrees F, but water was still liquid because the atmospheric pressure was so high due to the heavy CO~2~ in the atmosphere. The Earth continues to cool, the oceanic crust also cools. This is important because atmospheric carbon slowly gets removed through a process called **subduction**. This is where the oceanic crust is essentially recycled as a heavier plate is pushed below a lighter one down into the mantle. Not only does this process ultimately create land, but as carbon is taken up rocks as insoluble calcium carbonate it is slowly removed from the atmosphere.

![Subduction results in the formation of mountains, and also volcanoes and earthquakes. This diagram displays plate tectonics and the results of subduction in the Pacific Northwest ([Image source](https://www.nps.gov/subjects/geology/plate-tectonics-subduction-zones.htm).)](images/subduction.jpg){width="95%"}

### How did water get here? {-}

Okay, where were we? The moon has been formed by a violent blast. Volcanic activity is very high. We call this epoch the **Hadean** epoch, for Hades, or in other words, hell. I said previously that there was no liquid water during this time. However, there is still ongoing research to understand exactly when the atmosphere and oceans formed. For a long time, it was thought that there was no life or liquid water during the Hadean, but recent work is challenging that assumption.[^6] As of this writing, the origin of Earth's water is not definitively known.

![An artist's rendering of early Earth in the Hadean epoch. (Image from [Wikipedia](https://en.wikipedia.org/wiki/Hadean#/media/File:Hadean.png).)](images/hadean.png){width="75%"}

But here is a rough hypothesis. When the planetary body that created the moon hit Earth, a large portion of Earth's material was likely vaporized, possibly creating a "rock vapor" atmosphere. For the next few thousand years, this rock vapor atmosphere would have condensed, leaving behind an atmosphere heavy with CO~2~. It's also likely that this atmosphere contained hydrogen and water vapor. But how did the water vapor get there? It may be that icy planetary bodies orbiting around the sun smashed together to eventually become Earth, and the water was always here. Maybe it came from the giant impact that created the moon. Maybe an asteroid (or many, as Earth was hit often in early days) brought it. The point is, we're not entirely sure.

But as the Earth cools, the oceans condense, CO~2~ is pulled from the atmosphere by subduction, the magnetic field forms protecting us from heavy solar radiation---things become much more stable and favorable for biological life. The thing is, it might be possible to have very simple organisms in extreme conditions---which we will learn about soon. There are small bacteria that live in hot vents at the bottom of the ocean. But something like us multicellular mammals, we need _a lot_ of time and relatively stable conditions to emerge.

### The specialness of water {-}

Last week we discussed a property called electronegativity. We said that when elements share electrons, some elements pull those electrons closer to them giving them a slightly more negative charge. We called this a polar covalent bond. NH~3~ is one example, but the GOAT of polar covalent bonds has got to be water. Oxygen has much higher electronegativity compared to hydrogen, so it gives water a V shape. But because of the positive and negative charges on either end, it also makes water molecules attracted to _each other_ in weaker bonds called **hydrogen bonds**.


![Oxygen has a slightly negative charge while hydrogen has a slightly positive charge, due to electrons being pulled closer to oxygen. The positively charged hydrogen is attracted to the negatively charged oxygen.](images/waterbond.jpg){width="60%"}


Because of the atomic and molecular properties of water, there are six important and emergent features that make it especially perfect for supporting biological life. Water is also a wonderful place for chemical reactions to occur, and many reactions require the presence of water. This matters for the development of biological life on Earth.

1. **The states of water.** The weaker nature of hydrogen bonding gives water special properties as it changes from liquid to gas to solid ice. In liquid water, hydrogen bonds constantly form and break as the water molecules slide past each other. If we heat up the water, the increased motion of the water molecules (higher kinetic energy) causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas. If we cool the water instead to freezing temperatures, the water molecules form a crystalline structure that makes ice less dense than liquid water. Which leads us to...

2. **Ice is less dense than liquid water.** Have you ever noticed that when you add ice to your glass of water, it floats? That if a lake freezes over, the ice stays on top of the lake and doesn't sink to the bottom? This is a unique feature of water---many molecules are more dense as solids than as liquids, but water is the opposite! This is _very_ important for life, especially for the organisms that live in the lakes that freeze over. Imagine if ice sank: each winter, as the temperatures dropped below freezing, ice would sink to the bottom and the lake would eventually become a solid block of ice. Nothing could survive there. Instead, ice stays at the top, insulating the liquid water from the colder temperatures and protecting the creatures that live below.

3. **Water has a high specific heat.** Water has the highest specific heat capacity of _any_ liquid. What that means is that water can absorb A LOT of heat before it changes temperature. (Specific heat capacity is defined as the amount of heat that one gram of a substance must absorb to change its temperature by one degree Celsius.) It takes water a long time to heat up and a long time to cool down. This makes it the perfect substance to evenly disperse heat throughout our bodies and help us maintain our even temperature. This also means that it takes a lot of energy to turn water from a liquid into a gas...

4. **Water has a high heat of vaporization.** Heat of vaporization is the amount of energy that it would take to turn one gram of a liquid substance into a gas. It takes a lot of energy to disrupt water's hydrogen bonds and separate liquid water from itself, so water can act heat sink, absorbing lots of heat before turning into water vapor. As water heats up, hydrogen bonds are broken and water on the surface evaporates. This process absorbs energy (i.e., heat) meaning that evaporation can also facilitate cooling. Many animals use evaporative cooling mechanisms to regulate body temperature---or in other words, sweating!

5. **Water is a solvent.** Polar molecules are ones that have slightly positive and negative charges, just like water does. You may have heard the phrase "like dissolves like": this means that polar substances dissolve in other polar solutes (liquids), and nonpolar substances dissolve in nonpolar solutes. This is why when you add oil (nonpolar) to water (polar) one sits right on top of the other (unless you shake it up!).

6. **Cohesion and adhesion help transport water.** If you fill your glass of water a little too much, before it spills over the water will form a little dome at the top of the glass. This is because water molecules are attracted to each other via hydrogen bonding and this helps water "stick" to itself, a property called **cohesion**. Whereas cohesion refers to the tendency of the _same_ molecules to "stick" together, **adhesion** refers to the tendency of of _dissimilar_ particles or surfaces to "stick" together. 

We will continually see throughout this course how important water is for life on this planet. Now, just because us Earthlings evolved to need water does not necessarily mean that _any_ organism in the universe likewise needs water. But there are just no other substances that we know of that are as special as water in exactly the same way needed for the chemistry behind the business of life to occur. (We will learn a few more as we continue to discuss the emergence of life.) But first... what even _is_ this life thing?

\newpage

## 5: Defining Life {-}

We've so far spent all of our time discussing non-living (**abiotic**) entities. Atoms, elements, galaxies, planets. It is relatively easy for us, based on our intuition of living organisms, to say these things are not alive. But what does it mean to be "alive"? How do we actually define "life"? Why is a rock "not alive" and a coral "is alive"? I would encourage you to put down whatever device you are reading this from and think for a moment about how you would define **life**. Remember that this definition needs to encompass bacteria, plants, algae, all those weird sea creatures.

Let's start with a tricky case: a virus. A virus has impacted all of our lives dramatically for the last two years, but what even is a virus? A virus is simply genetic material stored inside some kind of case (an envelope or capsid), usually with a minimal number of proteins.


![Anatomy of the Coronavirus, consisting of an outer envelope, proteins, and genetic material. ([Image source](https://scienceexchange.caltech.edu/topics/covid-19-coronavirus-sars-cov-2/what-is-a-virus).)](images/corona.jpg){width=55%}

Is a virus alive? It can't do much without a host---it doesn't have any of the molecular machinery that the rest of us do, to read genetic material or make proteins. It can't capture energy or reproduce on its own. It is not made of cells. _But_. Once a virus gets inside its host, it can hijack the host's molecular machinery and use the host's energy to make copies of itself (reproduce) and spread to other hosts. A virus is even capable of evolving! Viruses that are not effective at infecting hosts and making copies of themselves will eventually disappear ("go extinct"). It's not exactly right to say that a virus is dead... but it's not exactly alive either. 

One of the craziest things to me is that **there currently exists no consensus on the definition of life**. One of the first challenges is whether or not we care about defining life _generally_, or defining life only within the context of Earth. Is all life mostly carbon based? Made of cells? Mostly made of water? Or is that just us freaks on this particular planet? One paper even put together 123 different definitions of the word "life."[^7] We can approach this from a philosophical standpoint, from a legal standpoint, from a biological standpoint, from a physics standpoint, from a systems standpoint. We can worry only about Earth or about life in the universe. We can include viruses or viroids or not include them.

### Emergence {-}

Life is trickier to define than say, a table:

>A piece of furniture usually supported by one or more legs and having a flat top surface on which objects can be placed.

See, a table is an object. While a table is a table, it does not fundamentally change. It is always a piece of furniture supported by legs with a flat top surface upon which we can put our crap. But life is not an object, life is _a process_. Organisms are born, grow, reproduce, and die. Organisms are constantly outside equilibrium with their surrounding environment, because as soon as you are at equilibrium with your environment you are dead. And it isn't just one thing, either. If something only grows but doesn't reproduce, that could be a mountain. If it captures energy but doesn't grow, that could be a car engine. So our definition needs to take into account not just one process, but many processes that go into sustaining living organisms through time.


![Ripples in sand or snow may be thought of as an emergent structure. On their own, sand grains or snow flakes cannot have this structure. But the interaction of individual grains and wind can cause this structure to emerge, taking on a property the individual components could not have on their own.](images/ripples.jpg){width=60%}


We say that life is an **emergent property**. What does that mean---emergence? We mean that life is a property that _emerges_ only through the interaction of components---like replication, or growth, or energy capture---which alone do not have this property. Life is sometimes described as an emergent property of chemistry, because all life is really just a bunch of atoms reacting in different ways, staying outside of chemical equilibrium. It is from these interactions that the property of life emerges.

### Why evolution matters {-}

Since we will start getting into the nitty-gritty of life for the rest of the course, it's important that we all understand some basics about how the evolution of living organisms actually works. First, we need to know that organisms are born with all the instructions for their parts---which is to say that an individual organism cannot change its own instructions (or DNA) during its lifetime. As much as I may think an extra finger would be really useful, I cannot grow myself an extra finger. I am stuck with the ten I was born with, based on the instructions coded in my DNA that I am unable to change.


![An organism is born with a specific set of instructions that they cannot change.](images/gene.jpg){width=65%}


The second is that only those features---or traits---coded for in our DNA instructions can be passed on to our offspring. If I lost a finger in a terrible accident, my offspring would not then be born without a finger. If I dye my hair purple, my children cannot be born with purple hair. I can't transmit a suntan, or a scar, or any characteristics that I acquired over my lifetime to my offspring. Only what's in my DNA, and losing a finger does not change my DNA.

We have an intuition that organisms _can_ pass on features that were acquired over their lifetime. Take the giraffe: it's easy to think that one giraffe stretched his neck a bit, passed on that stretched neck to its offspring, and so on, until the neck was very long. But we know that _cannot_ be the case, because organisms can only transit to their offspring what's in their DNA! And stretching your neck does not change your DNA. So then, how does this actually work?

![The distribution of human height, an example of variation within a species.](images/height.jpg){width=55%}


We observe that organisms in populations are varied in their traits. Think about human height: there are some folks that are pretty short, then medium, and then very, very tall. We are not all the same height but we vary. And not only that, height is partially determined by the instructions in our DNA, so height _is_ something that can be inherited. This is true about a lot of traits, in organisms across the tree of life---the traits are not the same in groups of organisms that belong to the same species. 


![If everyone over six feet tall dies, then they cannot reproduce or they reproduce less than those that are shorter. Over time, this changes the characteristics of the population. The change in heritable characteristics of a population over time is evolution.](images/height-marked.jpg){width=55%}


But let's imagine an extreme scenario. Let's say that anyone who is more than six feet tall gets their head chopped off by a vicious alien predator that now inhabits Earth. First, we lose everyone over six feet tall. But there are still the children of these people that will grow up to be six feet tall. But those children are unlikely to have children of their own, because maybe they reach six feet tall before they reach sexual maturity and they are unable to produce offspring before getting their heads chopped off. So very soon, maybe in a few generations, you will see a change in the population: no one is more than six feet tall. The folks that are more than six feet tall do not survive, and very few of them reproduce.

Now the folks that are less than six feet tall are fine. They have no issue surviving or reproducing, so they will leave behind more offspring than those that are six feet tall or more. Over generations, the characteristics _of the population_ change because folks with certain traits---they are shorter---leave behind more offspring relative to the folks that are taller. This change in the **heritable** (coded in our DNA) traits of a population over time is called **evolution**. (Technically, I have described **evolution by natural selection**, which leads to adaptations. In this case, being shorter than six feet is an adaptation because it provides an advantage in surviving and reproducing in this environment with alien predators. But not all evolution is adaptive! More on that later.)

Why am I describing all this? Because the change in heritable characteristics of a population over time is a defining feature of life. But it _only_ works if traits are heritable; that is, if the traits are coded in instructions that are passed to offspring. If there were no method of passing on instructions, how could there be life at all? Hopefully, by the end of this course, you'll fully appreciate how necessary heritability is for life, and how once you have heritability there will _always_ be evolution. Heritability binds us to our ancestors and constrains the possibilities available to future generations, leading to the dynamics described by evolutionary theory.

### From a biological perspective {-}

As biologists, we take a descriptive stance when defining life. Basically, we sort of describe what life is and use that as our definition. And that's going to work well enough for us in this course. For our purposes, all life is composed of **cells**. That is the building block upon which life is formed. Beyond that, here are the seven characteristics that most biologists agree are necessary components for life (from these together, life emerges):

+ **Homeostasis**: internal environment is regulated to maintain a constant state
+ **Organization**: made up of one or more cells
+ **Metabolism**: transform energy through chemical reactions
+ **Growth**: create more cellular components than are broken down
+ **Adaptation**: populations change over time in response to the environment, as some individuals leave more offspring than others
+ **Response to stimuli**: typically involve senses
+ **Reproduction**: the ability to produce new organisms

\newpage

## 6: Biological Molecules {-}

We learned, at least descriptively, what we think it means to be "alive" on this here planet Earth. But all that "alive" business---regulating the internal environment, organization, transforming energy, adapting, and so on---all living organisms use very specific molecules to carry out that business. Of course, I couldn't tell you what hypothetical alien life is made of or how it goes about capturing energy. But I can tell you that _every living creature on Earth_ is made of essentially the same stuff. Everything from the single-celled bacteria living on a root in a marsh to phytoplankton in the seas to the squirrels in our yards to you and me---we all are primarily composed of the same four kinds of molecules. (Even the same elements: just four elements---oxygen, carbon, hydrogen, and nitrogen---make up 96 percent of the human body's mass, and this is remarkably consistent across the tree of life.)

![The energy from the sun is harnessed by photosynthetic organisms like plants. These organisms store the energy from the sun in glucose (sugar) molecules, which other organisms consume.](images/poppy.jpg){width=65%}

I told you that the energy to power all life on Earth comes from the sun. But it's not like we lie out in the sun and recharge every day---so how do we actually get that energy from the sun inside of our bodies so that we can use it? We get it from the organisms that _do_ lie out in the sun and recharge all day; namely, plants. Through the process of photosynthesis (covered in Unit 3), plants capture the energy from the sun and store it in sugar molecules called glucose. This is the most basic, fundamental currency of energy used amongst living organisms. But what actually is it?

### Carbohydrates {-}

Carbon is special because of the configuration of its electrons. It has four free electrons---**valence electrons**---that are able to form covalent bonds. It can form double and triple bonds (share two or three electrons). Or, it can bond with four different elements. The point is that carbon is extremely flexible in its ability to form bonds and it forms the backbone of many important molecules.

![Carbon has four valence electrons, meaning it can form four covalent bonds. Four free electrons is the maximum number that an element can have, which means carbon is special. Here carbon is sharing its valence electrons with four atoms of hydrogen, making methane (CH~4~).](images/methane.png){width=40%}

At their very core, carbohydrates are really just sugar, plain and simple. But what is sugar? A collection of carbon atoms, hydrogen atoms, and oxygen atoms in various configurations. That's pretty much it, although it turns out that there are a _lot_ of different configurations that can be made with only these elements. What's important about sugar? Simple sugars, or **monossaccharide**, can be broken down by our cells to extract energy---pretty much every cell breaks down glucose for energy in a process called cellular respiration (which we will learn about in Unit 3). Monosacharrides are known as **monomers**, which are building blocks. Monomers are put together to form **polymers**, which include multiple building blocks. Two monosacharride monomers put together make a **disaccharide**.

![A review of carbohydrates, or sugars, and their function as biological molecules.](images/sugarover.jpg){width=75%}


Monosaccharides and disaccharides have a lot of stored energy in the carbon-hydrogen bonds, and these molecules are primarily used for energy in living organisms. But carbohydrates are also used for energy storage, usually in the form of **polysaccharides**, which are very long strings of monosaccharide building blocks (monomers). **Cellulose** is a good example, which forms the primary component of cell walls in plants. This carbohydrate is complex enough that us humans cannot digest it, although cows can (they have four stomachs!), which is why they eat grass and we do not.


### Lipids {-}

Next up on our tour, **lipids**, which include fats, phospholipids, and steroids. (We will focus on the first two.) Lipids are actually a pretty diverse set of molecules, but we group them together based on one important property: they are **nonpolar**. We talked about what **polar** means previously, which are molecules that share electrons unequally leading to slight positive and negative charges of the molecule itself. A polar molecule can easily dissolve another polar molecule based on the way their charged atoms interact. (For example, sugar is polar and dissolves easily in water.) You know what isn't polar? Oil. When you add oil to water, it just sits right on top.


![Oil and water don't mix. These two are polar opposites. Literally. Like oil and water. Okay, I'm done.](images/oil.jpg){width=25%}


That's because oil is a fat. A molecule of fat is constructed from **glycerol** and **fatty acids**. Three fatty acid molecules are each joined to glycerol, an type of alcohol. The resulting fat, also called a **triacylglycerol**, thus consists of three fatty acids linked to one glycerol molecule. The major function of fats is energy storage, as hydrocarbon chains are rich in energy. In **saturated** fats, every carbon is bound to hydrogen atoms, as many as it can be. But in **unsaturated** fats, there are one or more double bonds between carbon atoms---meaning that they are bound to fewer hydrogens. This also creates a "kink" in the chain meaning that these molecules cannot be packed very closely together. This is the reason why saturated fats---like butter---are solid at room temperature, while unsaturated fats---like olive oil---are liquid at room temperature.


![Saturated fats are "saturated" with hydrogen. Unsaturated fats have one or more double bonds meaning they are bound to fewer hydrogens. This creates a "kink" in unsaturated fats meaning they cannot be packed as closely together as saturated fats.](images/fats.png){width=40%}


One of the most important kinds of fats, **phospholipids** are the major component of cellular membranes. This means that every single cell in your body is contained by these special molecules! Phospholipids have two fatty acid molecules attached to a polar head. Oooh, interesting, polar _and_ nonpolar! The hydrophilic head interfaces with the aqueous (water-based) solution inside and outside of cells, while the hydrophobic non-polar tails face inward toward each other. This allows the formation of the **phospholipid bilayer**, consisting of two layers of phospholipids. The "head" portion consists of a phosphate group, along with a small charged or polar molecule like choline shown below. (There can be others, allowing for the formation of many different kinds of phospholipids.) 


![Phospholipids are made of two fatty acid tails and a polar head that includes a phosphate group. When placed in water, these molecules spontaneously form structures like bilayers and vesicles.](images/phospho.jpg){width=65%}


The last flavor of lipids are steroids, which includes cholesterol, another important component in membranes. We won't focus on these in class, but steroids also include a lot of biologically important molecules.


![A review of some lipid molecules.](images/fatreview.jpg){width=70%}


### Nucleic acids {-}

A lot of these molecules come from our diet. But our bodies also synthesize a lot of stuff too. How do our cells know how to make all the different "stuff" inside of us? Us organisms are primarily made from biological molecules called proteins, dicussed below. But how does a cell know how to make a protein in the first place? How does it know how to make just the _right_ protein? The instructions to build proteins are coded inside of **genes**, which are a discrete unit of inheritance. Genes are composed of **nucleic acids** (otherwise known as DNA), built from monomers called **nucleotides**. Nucleotides consist of (1) a five-carbon pentose sugar, (2) a nitrogenous (nitrogen-containing) base that gives the molecule a unique property, and (3) one to three phosphate groups.

![DNA and RNA are made from a sugar-phosphate backbone and nitrogenous bases.](images/nucleic.jpg){width=75%}

But DNA (**deoxyribonucleic acid**) is not directly involved in the production of proteins. There is another molecule called RNA (**ribonucleic acid**) that performs much of the work of transcribing and translating the information in DNA to an actual protein. You'll learn much more about these processes later. For now, we will focus on the structural components of DNA and RNA that allow these molecules to participate in processes necessary for life to function.

+ **Pentose sugar**. Nucleotides all have one pentose sugar, but the sugar in DNA lacks an oxygen atom on the second carbon ring, so we call it _deoxy_ribose. In RNA, the oxygen is there which is why it is simply ribose.

+ **Nitrogenous base**. There are two different kinds of nitrogenous bases. **Pyrimidines** have one carbon ring and there are three kinds: cytosine (C), thyamine (T), and uracil (U). **Purines** have two carbon rings and there are two kinds: adenine (A) and guanosine (G). (I usually remember the difference by the fact that the longer name, pyrimidine, has fewer rings.) T is only found in DNA while U is only found in RNA. The rest are found in both.

+ **Phosphate group**.  Three phosphate groups are attached to the 5$'$ carbon of the sugar, completing the nucleotide molecule. (If you look at the diagram of the ribose and deoxyribose sugars, you'll notice that the carbons of the pentose sugar are labeled. The 5$'$ carbon at the top binds with the phosphate groups, while the 3$'$ carbon at the bottom with the OH molecule is where the phosphate group of the next nucleotide will attach to join the nucleotides together. These numbers give the DNA or RNA molecule a certain directionality.)


![DNA is typically two complementary strands that run antiparallel to each other.](images/dnapair.png){width=42%}

DNA is typically consists of two strands of **polynucleotides** that wind around each other to form a **double-helix**. The two strands are bound to each other in the center by complementary base-pairing. Adenine always binds with thyamine in DNA or uracil in RNA. Guanine and cytosine always bind together. The strands run **antiparallel**, meaning that the sugar-phosphate backbones run in opposite directions. What do we mean by opposite direction? Well, the 5$'$ carbon holds the phosphate group, and the 5$'$ end can only be added to the 3$'$ of another nucleotide. That's the only place these molecules can be joined! Because of that, DNA and RNA have a 5$'$ carbon at the very top, and a 3$'$ carbon at the "butt" of the molecule. One strand runs 5$'$--3$'$ in one direction, and the other in the opposite, like the image above.


### Proteins {-}

_Proteins do everything_. I'm not kidding, proteins do nearly every job in a cell that you can imagine. They provide structure, storage, they transport substances within and between cells, they serve as receptors, catalyze chemical reactions, protect against disease, aid in movement, and respond to chemical stimuli. When we say that DNA is the "blueprint" for creating an organism, protein is _the thing_ for which DNA is laying out the plans (with some exceptions: it's biology!). You will learn more about the process by which DNA is read and proteins are constructed in Unit 4. For now, we will take a deep dive into the pieces of protein and how these pieces allow protein to do so many different jobs within an organism.

Proteins are made up of long chains of **amino acids**. There are twenty different amino acids that make up the proteins used by every living creature on Earth. Let that sink in. _Every living organism on the planet uses the same twenty amino acids, coded for by the same four nucleotides in our DNA._ All amino acids have the same basic structure, with an **amino group**, a **carboxyl group**, and the **R** group, which gives the molecule a special property. Below, highlighted in purple are the amino and carboxyl groups, and highlighted in yellow, green, pink, and blue are different R groups. Some side chains (or R groups) are hydrophobic, some are hydrophilic. Some are acidic, while others are basic. These varied properties mean that different combinations of amino acids can be used to build thousands and thousands of varied proteins, all with slightly different properties themselves.


![All twenty amino acids have the same basic structure. The R group or side chain differs between the different molecules, giving each a unique property.](images/aminoacidstructure.jpg){width=45%}



So how do we make a protein? At first it's pretty simple: we just add amino acids together in a long chain called a **polypeptide**. Making a polypeptide chain means linking amino acids together with a covalent bond called a **peptide bond**. Based on the way that amino acids link to each other, there will always be an amino end on one side (called the N-terminus) and a carboxyl group at the tail (called the C-terminus). In between the N- and C-termini are however many amino acids coded for in the gene for the protein.

The linear sequence of amino acids that form a protein is called its **primary structure**. But because amino acids each have special chemical properties, the polypeptide chain usually folds naturally into a conformation that gives the protein the ability to perform its function. Even tiny changes---substituting one amino acid for another in a polypeptide chain of hundreds of amino acids---can disrupt the protein's overall conformation and ability to function. 


![The primary structure of a protein is the linear sequence of its amino acids.](images/10-proteinstruc.jpg){width=29%}


The next layer of protein structure, **secondary structure**, results from repeated coils and folds into which long polypeptide chains can be organized. Because oxygen and nitrogen atoms in the amino acid backbone have a slight negative charge, these atoms can form hydrogen bonds with the weakly positive hydrogen atom attached to nitrogen. There are two common forms of secondary structure: the **alpha** ($\alpha$) **helix**, and the **beta** ($\beta$) **pleated sheet**. (Coils and folds!)


![From the linear sequence of amino acids, higher order structures emerge.](images/11_proteinstruc.jpg){width=75%}


Tertiary structure consists of more irregular contortions that result from bonds between different R groups. As a polypeptide chain begins to fold, hydrophobic side chains usually congregate together in clusters at the center of the protein, called **hydrophobic interactions**. Hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains can also stabilize this structure. Finally, proteins can have one final layer of structure called **quaternary** structure. This occurs when two or more polypeptide chains aggregate together to form one large molecule with multiple subunits.


### Miller-Urey experiment {-}

This experiment is famous. Very famous. The idea behind it is simple: what happens if we emulate the conditions of early Earth? Would it be possible to observe the formation of any biological molecules? Miller and Urey used the same gases thought to exist in Earth's early atmosphere (methane, hydrogen, water vapor, and ammonia). Electrodes simulated possible lightning. Water, from the "ocean" was heated and directed toward the "atmosphere," cooled in a condenser, and what remained was collected.


![The set-up of the Miller-Urey experiment.](images/millerurey.png){width=49%}


From just this, several amino acids were recovered, the building blocks of proteins. This experiment demonstrated that biological molecules may emerge from purely chemical reactions in early Earth. But the truth is, we don't yet know how life emerged from non-living entities. We will spend the rest of the course examining the various hypotheses while we explore the important features common to all living organisms.

<!-- + All living (whatever life is) organisms are essentially made of the same stuff -->
<!-- + Talk about the importance of carbon here -->
<!-- + Carbohydrates provide energy -->
<!-- + Nucleic acids store information -->
<!-- + Proteins made of amino acids do it all -->
<!-- + Lipids, while not technically polymers, form all our membranes -->
<!-- + Miller and Urey showed you could make some of this stuff based on what was available on early earth -->


[^1]: Mass versus weight: https://sciencenotes.org/mass-vs-weight-the-difference-between-mass-and-weight/
[^2]: There are six kinds of quarks, called "flavors." You don't need to know that, but I think it's funny. The quarks come in the flavors of up, down, charm, strange, top, and bottom.
[^3]: We won't touch on how we know it's there in class, but you can always [check out YouTube](https://www.youtube.com/watch?v=uBbxXNhZ78c).
[^4]: Not every star runs on hydrogen, but ours does, and the stars of the early universe did, so we'll focus on that.
[^5]: Quantum fluctuations are basically randomness in the energy distribution of particles.
[^6]: https://www.science.org/doi/10.1126/science.aba1948
[^7]: https://www.tandfonline.com/doi/abs/10.1080/073911011010524992