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Add graphic showcasing evolution of life (#270)

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* Add graphic showcasing evolution of life

* Add PR Feedback

* Add comment

* Update date format

* Fix small mistakes

* Add pangea, rewrite intro

* Fix citation, improve intro. Thanks alanblue

* Add indicator for full span and months

* Color improvements
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Hendrik Kleinwaechter
2023-11-07 21:52:23 +01:00
committed by GitHub
parent afc9e37229
commit 8640ed18ed
4 changed files with 174 additions and 5 deletions
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70
book/figures/fig-life-planet-sourdough-timeline.tex Normal file
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@@ -0,0 +1,70 @@
\begin{tikzpicture}
% Draw horizontal line
\draw[line width=1pt] (0,0) -- (\textwidth,0);
% Define the width of each segment
\pgfmathsetlengthmacro{\segmentwidth}{\textwidth/12}
% Draw lines for the events, higher up so that they don't overflow the text
% Placing the lines has been a bit manual work of trying different values
% Maritime bacteria.
\draw[line width=1pt] (2.8*\segmentwidth,1) -- (2.8*\segmentwidth,0.2);
% Eukaryotes
\draw[line width=1pt] (5.8*\segmentwidth,1.5) -- (5.8*\segmentwidth,0.2);
% First bacteria on land
\draw[line width=1pt] (9.1*\segmentwidth,-1.25) -- (9.1*\segmentwidth,-0.2);
% Maritime fungi ancestors
\draw[line width=1pt] (9.5*\segmentwidth,-2) -- (9.5*\segmentwidth,-0.2);
% Fungi on land
\draw[line width=1pt] (10.8*\segmentwidth,-2.75) -- (10.8*\segmentwidth,-0.2);
% Yeasts on land
\draw[line width=1pt] (11.1*\segmentwidth,-3.0) -- (11.1*\segmentwidth,-0.2);
% First dinosaurs
\draw[line width=1pt] (11.4*\segmentwidth,0.5) -- (11.4*\segmentwidth,0.2);
% Pangea begins to rift apart
\draw[line width=1pt] (11.6*\segmentwidth,1) -- (11.6*\segmentwidth,0.2);
% Dinosaur extinction
\draw[line width=1pt] (11.9*\segmentwidth,1.5) -- (11.9*\segmentwidth,0.2);
% Special lines for december events since they are so close togehter
\draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (12.0*\segmentwidth,0.2); % Main branch
\draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (11.75*\segmentwidth,2.5); % Branch to first humans
\draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (11.75*\segmentwidth,3.0); % Branch to Jordan
\draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (11.75*\segmentwidth,3.5); % Branch to Pasteur
% Draw months and month separators
\foreach \i/\month in {0/Jan, 1/Feb, 2/Mar, 3/Apr, 4/May, 5/Jun, 6/Jul, 7/Aug, 8/Sep, 9/Oct, 10/Nov, 11/Dec} {
% Separators
\draw[line width=1pt] (\i*\segmentwidth,0.1) -- (\i*\segmentwidth,-0.1);
% Month names
\node[timeline_event, below] at ({(\i+0.5)*\segmentwidth},-0.1) {\month};
}
\draw[line width=1pt] (\textwidth,0.1) -- (\textwidth,-0.1);
% Full timeline width for billion years
\draw[line width=1pt] (0,-3.8) -- node[midway, timeline_timespan] {5.45 billion years} (\textwidth,-3.8);
\draw[line width=1pt] (0,-3.7) -- (0,-3.9);
\draw[line width=1pt] (\textwidth,-3.7) -- (\textwidth,-3.9);
% Indicator for the period of 3 months = 1.1 billion years
\draw[line width=1pt] (0,-1.0) -- node[midway, timeline_timespan] {1.11 billion years} ({\segmentwidth * 3},-1.0);
\draw[line width=1pt] (0,-0.9) -- (0,-1.1);
\draw[line width=1pt] ({\segmentwidth * 3},-0.9) -- ({\segmentwidth * 3},-1.1);
% Place events on the timeline with dates using the timeline_event style
% As a calculation I used (4.54 billion years / 12 months = 0.3785 billion years/month.
\node[timeline_event, above] at (2.0*\segmentwidth,1) {Mar 25 - First maritime bacteria and archae};
\node[timeline_event, above] at (4.50*\segmentwidth,1.5) {June 25 - First organisms with nuklei (eukaryotes)};
\node[timeline_event, above] at (7.8*\segmentwidth,-1.5) {Oct 4 - First bacteria on land};
\node[timeline_event, above] at (8.0*\segmentwidth,-2.25) {Oct 15 - First maritime ancestors of fungi};
\node[timeline_event, above] at (9.7*\segmentwidth,-2.75) {Nov 24 - Fungi on land};
\node[timeline_event, above] at (10.5*\segmentwidth,-3.25) {Dec 3 - Yeasts on land};
\node[timeline_event, above] at (10.2*\segmentwidth,0.5) {Dec 14 - First dinosaurs};
\node[timeline_event, above] at (9.8*\segmentwidth,1) {Dec 17 - Pangea begins to rift apart};
\node[timeline_event, above] at (10.33*\segmentwidth,1.5) {Dec 29 - Dinosaurs go extinct};
\node[timeline_event, above, anchor=east, align=right] at (11.75*\segmentwidth,2.5) {Dec 31 - First humans};
\node[timeline_event, above, anchor=east, align=right] at (11.75*\segmentwidth,3.0) {Dec 31 - Sourdough in Jordan (23:59:55)};
\node[timeline_event, above, anchor=east, align=right] at (11.75*\segmentwidth,3.5) {Dec 31 - Louis Pasteur isolated yeast (23:59:59)};
\end{tikzpicture}

5
book/figures/flowcharts_tikz.tex
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@@ -25,3 +25,8 @@
decoration={calligraphic brace, amplitude=3mm, raise=1mm}, decoration={calligraphic brace, amplitude=3mm, raise=1mm},
very thick, pen colour={black} ] very thick, pen colour={black} ]
\tikzstyle{loop} = [arc, draw=codeblack, line width=0.4mm] \tikzstyle{loop} = [arc, draw=codeblack, line width=0.4mm]
\tikzstyle{timeline_event}=[align=center, fill=white, inner sep=2pt]
\tikzstyle{timeline_timespan} = [rectangle, draw=codeblack, fill=pinkpic, text=black,
text centered, rounded corners, line width=0.4mm]

77
book/history/sourdough-history.tex
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@@ -9,11 +9,78 @@
lessons from the past. lessons from the past.
\end{quoting} \end{quoting}
Sourdough has been made since ancient times. The exact origins of fermented The story of sourdough bread begins in prehistoric oceans. These oceans were the
birthplace of all life on Earth. To better envision the vast history of
our planet, lets create a timeline in one~year/365~days. On this scale,
January~1 signifies Earth's
formation 4.54~billion years ago. Midnight on December~31 is the present.
Each day represents roughly 12~million years. This technique simplifies the
complexity of time but also renders the extraordinary expanse of our planet's
history into a more graspable timeframe. We humans, are in fact a recent
addition to our planet, so young that we made our first appearance on
the evening of December~31. It seems that humans managed to arrive just
in time to join the celebration at the end of the year.
The story of sourdough bread begins in ancient oceans. These oceans were the
birthplace of all Earth's life. To better envision the vast history of
our planet lets create a timeline of 1~year. On this scale, January~1 signifies Earth's
formation 4.54~billion years ago. Midnight on December~31 is our present.
Each day represents roughly 12~million years. This technique simplifies the
complexity of time but also renders the extraordinary expanse of our planet's
history into a more graspable frame. We humans are in fact a recent addition
to our planet, so young that we made appearance on the evening of December~31.
It seems that humans managed to arrive just in time to join
the celebration at year's end.
On March~25, the oceans birthed the first single-celled bacteria. In these
waters, another single-celled life form, \emph{archaea}, also thrived. These
organisms inhabit extreme environments, from boiling vents to icy waters.
\begin{figure}[!htb]
\begin{center}
\input{figures/fig-life-planet-sourdough-timeline.tex}
\caption[Sourdough microbiology timeline]{Timeline of significant events
starting from the first day of Earth's existence,
divided into months, and extending to the present day,
marked at midnight. This visualization shows the pivotal steps
of life and sourdough on earth.}%
\end{center}
\end{figure}
Whoever comes first first, bacteria or archaea, remains debated. For three
months (or approximately 1.1~billion years), these life forms dominated
the oceans. Then, on June~25 in an highly unlikely event, an archaeon consumed a bacterium.
Instead of digesting it, they formed a symbiotic relationship. This led to the
first nucleated organisms, marking an evolutionary milestone. This event lead
to the development of plants, fungi and also ultimately humans.
Life stayed aquatic for another three months.
On October~4, bacteria first colonized land. By October~15, the
first aquatic fungi appeared. They adapted and, by November~24, had colonized
land.
By December~3rd, yeasts emerged on land. This laid groundwork for bread-making.
Jump 140~million years to December~14, and dinosaurs arose. Just a couple
of days after their appearance on December~17 the super continent pangea
started to rift apart, reshaping the continents into their current form.
The dinosaurs reigned until December~29 when they faced extinction.
Another 25~million years later, or our timeline's 2~days after the dinosaur
extinction, humans appeared.
A few hours later after the arrival of humans, a more subtle culinary
revolution was unfolding. By \num{12000}~BC, just 5 seconds before our metaphorical
midnight, the first sourdough breads were being baked in ancient Jordan. A blink of
an eye later, or 4~seconds in our time compression, Pasteur's groundbreaking work
with yeasts set the stage for modern bread-making. From the moment this book
began to take shape to your current reading, only milliseconds have ticked by~\cite{Yong_2017}.
Now delving deeper into the realm of sourdough, it can likely be traced to aforementioned
Ancient Jordan~\cite{jordan+bread}. Looking at the earth's timeline sourdough
bread can be considered a very recent invention.
The exact origins of fermented
bread are, however, unknown. One of the most ancient preserved bread are, however, unknown. One of the most ancient preserved
sourdough breads has been excavated in Switzerland. sourdough breads has been excavated in Switzerland~\cite{switzerland+bread}.
However, based on recent research, some scientists speculate that sourdough
bread had already been made in \num{12000}~BC in ancient Jordan~\cite{jordan+bread}.
\begin{figure}[ht] \begin{figure}[ht]
\includegraphics[width=\textwidth]{einkorn-crumb} \includegraphics[width=\textwidth]{einkorn-crumb}
@@ -28,7 +95,7 @@ dough and at her return a few days later, she noticed that the dough had
increased in size and smelled funky. She decided to bake increased in size and smelled funky. She decided to bake
the dough anyway and was rewarded with a much the dough anyway and was rewarded with a much
lighter, softer, better tasting bread dough. From that day lighter, softer, better tasting bread dough. From that day
on she continued to make bread this way. on she continued to make bread this way~\cite{egyptian+bread}.
Little did the people back then know that tiny microorganisms Little did the people back then know that tiny microorganisms
were the reason the bread was better. It is not clear when were the reason the bread was better. It is not clear when

27
book/references.bib
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@@ -98,6 +98,33 @@
howpublished = {\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077754/}} howpublished = {\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077754/}}
} }
@article{switzerland+bread,
author = {Pasquale Catzeddu},
title = {Flour and Breads and their Fortification in Health and Disease Prevention},
pages = {37--46},
year = {2011}
}
@book{Yong_2017,
place = {London},
title = {I contain multitudes: The microbes within US and a grander view of life},
publisher = {Vintage},
author = {Yong, Ed},
year = {2017},
pages = {5--9}
}
@article{egyptian+bread,
title = {Investigation of ancient Egyptian baking and brewing methods by correlative microscopy},
volume = {273},
DOI = {10.1126/science.273.5274.488},
number = {5274},
journal = {Science},
author = {Samuel, Delwen},
year = {1996},
pages = {488–490}
}
@article{vienna+breadrolls, @article{vienna+breadrolls,
author = {Eben Norton Horsford}, author = {Eben Norton Horsford},
title = {Report on Vienna bread}, title = {Report on Vienna bread},