From 8640ed18edb154146b1fe85c81996ba3b9de6885 Mon Sep 17 00:00:00 2001 From: Hendrik Kleinwaechter Date: Tue, 7 Nov 2023 21:52:23 +0100 Subject: [PATCH] Add graphic showcasing evolution of life (#270) * 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 --- .../fig-life-planet-sourdough-timeline.tex | 70 +++++++++++++++++ book/figures/flowcharts_tikz.tex | 5 ++ book/history/sourdough-history.tex | 77 +++++++++++++++++-- book/references.bib | 27 +++++++ 4 files changed, 174 insertions(+), 5 deletions(-) create mode 100644 book/figures/fig-life-planet-sourdough-timeline.tex diff --git a/book/figures/fig-life-planet-sourdough-timeline.tex b/book/figures/fig-life-planet-sourdough-timeline.tex new file mode 100644 index 0000000..0db4ee7 --- /dev/null +++ b/book/figures/fig-life-planet-sourdough-timeline.tex @@ -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} diff --git a/book/figures/flowcharts_tikz.tex b/book/figures/flowcharts_tikz.tex index ece37e2..5a8bb6a 100644 --- a/book/figures/flowcharts_tikz.tex +++ b/book/figures/flowcharts_tikz.tex @@ -25,3 +25,8 @@ decoration={calligraphic brace, amplitude=3mm, raise=1mm}, very thick, pen colour={black} ] \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] diff --git a/book/history/sourdough-history.tex b/book/history/sourdough-history.tex index f767f98..a7fbf4f 100644 --- a/book/history/sourdough-history.tex +++ b/book/history/sourdough-history.tex @@ -9,11 +9,78 @@ lessons from the past. \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 -sourdough breads has been excavated in Switzerland. -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}. +sourdough breads has been excavated in Switzerland~\cite{switzerland+bread}. \begin{figure}[ht] \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 the dough anyway and was rewarded with a much 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 were the reason the bread was better. It is not clear when diff --git a/book/references.bib b/book/references.bib index 39e1c6d..6184dc4 100644 --- a/book/references.bib +++ b/book/references.bib @@ -98,6 +98,33 @@ 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, author = {Eben Norton Horsford}, title = {Report on Vienna bread},