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Maybe you recognize this scenario. You have 10+ Stack Overflow tabs open and are running Git commands that you don't really understand. I've been there. Several times, and I hated it.

I needed a better mental model of how Git worked. This is the article I would have written to safe myself from a lot of uncertainty. Together we'll build a concise mental model of Git. So when things do go south, you know why you'll have to run certain commands to fix things. Let's dive in!

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Let's start with the command `git init` to add Git to this project.

<InnerWorkingsTerminal step={0} expectedCommand="git init" />

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  We can see that there is a `.git` folder created in our repository. Let's
  create an empty text file. We do this with the command `touch`. Let's run the
  command `touch text.txt`.
  <InnerWorkingsTerminal step={1} expectedCommand="touch text.txt" />
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  Awesome! We now have created an empty text file called `text.txt`. Let's see
  what Git thinks of this newly created file by running the command `git
  status`.
  <InnerWorkingsTerminal step={2} expectedCommand="git status" />
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  The status command tells us that the `text.txt` file is **untracked**. Files
  in our repository can be **tracked** and **untracked**. We just created the
  `text.txt` file, so we need to inform Git of its existence. We do this by
  running the command `git add text.txt`.
  <InnerWorkingsTerminal step={3} expectedCommand="git add text.txt" />
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Awesome, Git now knows of the existence of our file. Conceptually we have added it from our <Badge color="blue">working directory</Badge> to the <Badge color="green">staging area</Badge>. This is the place where we add the changes that we would like to save to the <Badge color="yellow">repository</Badge>. We can save our progress with a commit. But before we do that, let's look further into what just happened.

When we ran `git add text.txt` Git copied the file to the .git/objects directory. But it didn't just copied the text.txt file. It has been transformed to a _Blob_, which stands for binary large object. A format used to store files. Blobs are one of four types that Git uses. The other types are trees, commits and annotated tags. The most important are the blobs, trees and commits. We will explore these in depth. So, back to our newly created Blob!

In the objects folder a new folder has appeared. It has `e6` as a name and in it is our blob file called `9de29bb2d1d6434b8b29ae775ad8c2e48c5391`. Now the folder and file name are not random. Git uses a Secure Hash Algorithm (SHA) to hash the content of our text.txt file. The output is a 40 character string. The first two characters become the folder and the rest of the string become the filename.

The output of a SHA is always consistent. The same input will always get you the same output. Try commiting an empty file in your own Git project and you will end up with the exact same folder and file name. We will see further on why this is important.

So let's run `git status` again to see how Git is feeling about our new file.

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So Git tells us that we have a new file to commit. A commit takes all the changes in our staging area and saves them to our repository. It saves the state of our reposity with a snapshot of the whole project.

So our staging area is like a place for the rough drafts that we make. When we are sure of the changes we can commit the changes.

So let's do that by running the command `git commit -m "your commit message"`.

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Next steps:

- Explaining what happened under the hood when we just ran `git commit`.
  - When we ran git commit we made a snapshot that captures the state of our entire project in this exact moment.
  - Show what object have been added (tree and commit) and how we can check what they contain (plumbing commands)
  - Git is divided in plumbing and porcelain command. You are probably familiar with the porcelain commands. The plumbing commands are the ones giving insight into the inner workings of git. Other more user-friendly commands are made by stringing these together (like git pull, which is git fetch and git merge together).
- I also want to clearify these concepts
  - What is a remote?
  - What is an origin?
  - What is a HEAD?
  - How does branching work?

https://www.youtube.com/watch?v=lG90LZotrpo&t=1086s

as

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A deep dive into the magic that powers Git

The inner workings of Git


The Milky Way. The current estimation is that there are at least 100 billion stars in it. A billion stars is an incomprehensible amount. Let alone a hundred of them. It doesn't fit into my head. And what is even more mind-bending is that we all carry a much bigger galaxy within ourselves.

Every human is a walking vessel with a galaxy of dozens of trillions of living organisms. Those organisms are bacteria. In fact, there are more bacteria than cells in our body. We are being outnumbered.

## The coolest time in the timeline

Although bacteria have a bad reputation, we actually work together quite well. For generations, we have harnessed their power to create more preservable food. We did this with a process called fermentation.

The increased preservability meant you could keep food for months instead of days. This made fermenting food very popular. Hence why we find it in every culture and its kitchen.

But the world changed. Refrigerators came on to the scene. They made it easy to preserve food and the necessity to ferment food to preserve it decreased. But we were in too deep. The bacteria had already formed our food culture. And as it was our culture, so it was theirs.

Fermentation is here to stay. The world's cuisines wouldn't be the same without it. From Yogurt to cheese. Sourdough bread to salami. Sauerkraut to Kimchi. Fermented food is everywhere.

<Image
  src="bacteria-rule-the-world.png"
  alt="Illustration of the globe with bacteria on it"
/>

## Living Foundation of Life

So what does it mean when something ferments?

Biologists describe the process as anaerobic metabolism. Metabolism is the process that occurs within a living organism to maintain life. Anaerobic means without oxygen. So it is the process of creating energy from nutrients without oxygen.

The earth's atmosphere didn't always have oxygen. But fermenting bacteria don't need oxygen. That is why it is thought that they emerged early in the timeline of life. And with their emergence came quite a big role, as they were the sole inhabitants of earth.

For the first two billion years of life on Earth bacteria were the inventors of the planet. They created all life's essential chemical systems.

From this foundation the rest of life on earth flourished. All life is built upon them. But our relationship to them doesn't reflect this.

Most people see bacteria as something dirty and insignificant. Not as something that everything emerged from.

Now this is not me saying that you should stop washing your hands. Only some (fermented) food for thought on our relationship towards them.

## Is you inner metropolis thriving?

Microbes cover every spec of your body, inside and out. Your skin, blood vessels and organs are all populated with their own microbiomes. Communities of microbes living together. But there is one place that contains more bacteria than any other: your gut microbiome.

You can think of the microbiome as the bustling bacteria metropolis of the body. It contains many different species living and working together. Together they work to support health and well-being.

A city relies on its inhabitants to thrive and grow. The gut works the same. The health of the microbiome depends on its diverse community of bacteria.

Just as a city is being affected by external factors, the gut microbiome is a living changing system. It adapts by the food we eat, the medications we take, and other elements of our environment.

## Hey Siri, play HUMBLE by Kendrick Lamar

As humans we feel like we have dominated nature. We stand above it. We see this reflected in the definition of the word 'Nature':

_The phenomena of the physical world collectively, including plants, animals, the landscape, and other features and products of the earth, as opposed to humans or human creations._

Comedian George Carlin has [a very fitting piece](https://www.youtube.com/watch?v=7W33HRc1A6c) about this attitude. We are not separated from nature and we could definitely be more humble. We can see this attitude of superiority in so many of our relationships to parts of nature.

Michael Pollan wrote in his book "The botany of desire" about the idea of us dominating plants. Contrary to popular belief, we might not be using plants as much as plants use us. They ensure their survival by appealing to our human desires. Using beauty, sweetness, intoxication and control.

It is a different way of looking. A very interesting one that shifts the dynamics of power.

## The Free Will of your Bacteria

As humans, we often believe that we are in control and that we are the masters of our own destiny. That there is a distinct ‘self’ or ‘I’ that exists within us. Yet, this belief can be challenged.

What about the influence of the trillions of bacteria that live inside our bodies? These bacteria are interacting with our bodies.

They influence our health, thoughts and behaviours. This shifts the power dynamic. It reminds us that we are not as independent, separate and self-sufficient as we might think.

Research<sup>[1]</sup> has shown that the gut microbiome has a profound impact on the brain and behaviour. The gut bacteria produce a variety of chemicals influencing the brain.

Research shows that the "gut-brain axis" influences mood, behavior, and cognitive function. Imbalances in the gut microbiome have been linked to conditions such as anxiety, depression, and even autism.

Furthermore, the gut microbiome plays a key role in the immune system. Disruptions to it are associated with a range of autoimmune diseases.

Therefore, maintaining a healthy gut microbiome is essential for overall health and well-being. And it actually makes it easier to make healthier choices when your gut flora is healthy. Let's see why.

## Is It You That Is Craving That Ice Cream?

Bacteria play a vital role in the digestion of food in the human body. They help to break down the food we eat by creating enzymes. A healthy and balanced gut microbiome is essential for a good digestive system.

Your gut microbiome will adapt to your food intake. So when you feed yourself, you are also feeding entire cultures of bacteria. And they will let you know what they preference.

You might think that it is you that is craving that bowl of ice cream. But, there is a big chance that there are millions of hungry bacteria in your gut screaming for it.

An example of this is when your diet is high in refined sugar. All of this sugar can feed the harmful bacteria, which then can disrupt the balance of your gut microbiome. So when your diet contains a lot of sugar and you quit eating sugar all of a sudden, you're literally starving millions of bacteria. And they won't give up without a fight.

## Take Care of Your Microbial Cultures and They Will Take Care of You

It was the year 1928 when Alexander Fleming invented penicillin, the first antibiotic. An immeasurably important discovery that was a true turning point for healthcare. But it also came with a downside. Antibiotics do not discriminate. The antibiotic word has its origin in the Latin anti, which means against, and biotic, which means pertaining to life. It kills the harmful, but the beneficial bacteria as well.

This heavily effects your gut microbiome. The bacteria in your gut microbiome keep each other in check. So when you kill a huge part of your gut flora things can go awry. Bad bacteria can get the overhand quick, resulting in an imbalance. This is being called gut dysbiosis.

When you wipe out the majority of the existing culture, overgrowth of harmful bacteria can happen fast. It also reduces biodiversity, which is vital to a healthy and balanced microbiome.

[1] [https://www.nature.com/articles/s41579-020-00460-0](https://www.nature.com/articles/s41579-020-00460-0)


A deep dive into my fascination for the microbial live and their role in ours.

The Inner Workings of Git.