:clown:

Author: Lucy Delaney

.gitignore

@@ -4,6 +4,8 @@
 04-heredity.Rmd
 05-reproduction.Rmd
 
+_book/
+
 # History files
 .Rhistory
 .Rapp.history

01-birth.Rmd

@@ -16,7 +16,7 @@ Why we care is a complicated question with no singular answer, but I think we ou
 
 ## 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 85 percent of the matter in the universe is invisible to the entire electromagnetic spectrum, including all of human visible light. We call this matter **dark matter**, 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]
+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%"}
@@ -109,7 +109,7 @@ Between 10-20 seconds following the Big Bang, protons and neutrons are finally a
 
 ### 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 (four protons and four neutrons), and lithium-7 (seven protons and seven neutrons). But for the next 370,000 years, the universe is still too hot and too dense to form a bona-fide atom. And 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.
+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.
 
@@ -157,7 +157,7 @@ Some atoms pull electrons toward themselves more than other atoms, a property ca
 
 ## 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 theory 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 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%}
@@ -230,7 +230,7 @@ Right now, on early Earth, right after the giant impact, the scene is very, very
 
 ## 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 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.
+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.
 
@@ -320,7 +320,7 @@ We say that life is an **emergent property**. What does that mean---emergence? W
 
 ### 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 five I was born with, based on the instructions coded in my DNA that I am unable to change.
+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%}
@@ -409,7 +409,7 @@ The last flavor of lipids are steroids, which includes cholesterol, another impo
 
 ### 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), build 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.
+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%}
 
@@ -429,7 +429,7 @@ DNA is typically consists of two strands of **polynucleotides** that wind around
 
 ### 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, accelerate 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 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.