Jekyll2022-08-08T10:41:06+01:00https://bcmoon.uk/feed.xmlBen MoonA palaeontologist with a penchant for things that swimBen MoonNew Palaeogeographical Maps in R2022-01-13T00:00:00+00:002022-01-13T00:00:00+00:00https://bcmoon.uk/palaeontology/new-palaeogeographical-maps<p>I’ve added a new research page linked from my <a href="/">homepage</a> and the first thing up is an extended workshop that I ran on <a href="/palaeomap/01-introduction/">plotting palaeogeographical maps and occurrence data using GPlates, the PBDB, and R</a>. Have a look and let me know if you find it useful.</p>
<p>Eventually I’ll add more about my research: plans, projects, code, etc.</p>
<p>But for now I wish you a happy start to 2022.</p>Ben MoonI’ve added a new research page linked from my homepage and the first thing up is an extended workshop that I ran on plotting palaeogeographical maps and occurrence data using GPlates, the PBDB, and R. Have a look and let me know if you find it useful.Brunel Lockdown Project: _New World Symphony_2021-04-12T00:00:00+01:002021-04-12T00:00:00+01:00https://bcmoon.uk/music/largo-lockdown-projectBen MoonBuilding Palaeogeographic Maps in R2021-02-16T00:00:00+00:002021-02-16T00:00:00+00:00https://bcmoon.uk/palaeontology/palaeomaps-in-R<p>At the end of last year, I was looking at data from the <a href="https://paleobiodb.org/#/">Palaeobiology
Database</a> (PBDB) and wanted to draw a map of where
fossils were found. I made such maps for Jurassic ichthyosaurs before, which
appeared in Moon & Kirton (2018, Fig. 46). These I made by hand, tracing maps
from Blakey (2008, 2014) then overlaying palaeo-positions of various
ichthyosaur finds. As I remember, the tracing itself was not too time consuming,
but wasn’t the most interesting thing I’ve ever done.</p>
<p>Now I wanted to create maps with many more points and show a series of
time slices as the position of the continents change. This would definitely
benefit from a more automated method rather than me getting annoyed doing it all
manually.</p>
<p>Fortunately there are ways to do this in R with code and packages that
are readily available. Here’s a little intro to how I’ve made a map with data
from the PBDB, including:</p>
<ul>
<li>plotting continent and coastal outlines</li>
<li>adding points to show occurrence locations</li>
<li>separating different groups into subplots.</li>
</ul>
<p>In this case I’ll plot data of Toarcian (182.7–174.1 million years ago, Ma)
ichthyosaurs. Let’s dive in.</p>
<h3 id="data-gathering">Data gathering</h3>
<p>The few things that we need are:</p>
<ul>
<li>Occurrence data from the Palaeobiology Database</li>
<li>Palaeogeographic outlines of the continents at a desired time.</li>
</ul>
<dl>
<dt>Fossil occurrences</dt>
<dd>Finds of species at a single time and place. In the Palaeobiology Database
these are linked to <em>collections,</em> which are groups of fossil finds from a
single effort, like a single fossil dig.</dd>
<dt>Palaeogeography</dt>
<dd>The ancient configuration of continents, coastlines, mountains and seas
changing with continental drift and sea level change.</dd>
<dt>Palaeocoordinate</dt>
<dd>The ancient position of modern locations. Modern locations have
a latitude and longitude value, while palaeocoordinates have palaeolatitude
and palaeolongitude. These can be reconstructed using the relative movement of
continental plates from the present back through the past.</dd>
</dl>
<p>The PBDB has a <a href="https://paleobiodb.org/data1.2/">Web API</a>, which I find the
easiest way to download data. There is also the package
<a href="https://github.com/ropensci/paleobioDB">ropensci/paleobiodb</a>, but I haven’t
used it myself. Or you can download a CSV file direct from the portal.</p>
<p>To download occurrences of ichthyosaurs from the Toarcian I used the following
code in R.</p>
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">library</span><span class="p">(</span><span class="n">tidyverse</span><span class="p">)</span><span class="w">
</span><span class="n">pbdb_url</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="s2">"https://paleobiodb.org/data1.2/occs/list.csv?base_name=Ichthyosauromorpha&interval=Toarcian&show=paleoloc"</span><span class="w">
</span><span class="n">occ_toarcian_ichthyosaurs</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="n">readr</span><span class="o">::</span><span class="n">read_csv</span><span class="p">(</span><span class="n">pbdb_url</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>
<p>In looking for outlines of ancient continents, I found a few sources. First, I
came across the R package <a href="https://github.com/NonaR/paleoMap">NonaR/paleoMap</a>,
which includes map data and functions for organising them within the package.
But this was last updated in 2015, so may be a little out of date now or may use
functions not in the more recent versions of R. (I admittedly did not take too
long to check.)</p>
<p>After, I found <a href="https://github.com/LunaSare/gplatesr">LunaSare/gplatesr</a>.
gplatesr downloads data from the <a href="https://gws.gplates.org">GPlates Web Service</a>,
and can reconstruct palaeocoordinates – something I look forward to reading up
on and using more.</p>
<p>Getting this data into R is straightforward: using code from the package
gplatesr as a cue, these following lines download outline data for the
continents at 182 Ma, in the early Toarcian. In this case, I wanted both the
positions of the continental plates (static polygons) and the coastlines. The
package <em>rgdal</em> reads in the data and organises it into a structure that R can use
and understand.</p>
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">library</span><span class="p">(</span><span class="n">rgdal</span><span class="p">)</span><span class="w">
</span><span class="n">coastline_gws_url</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="s2">"http://gws.gplates.org/reconstruct/coastlines/?time=182&model=GOLONKA"</span><span class="w">
</span><span class="n">polygons_gws_url</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="s2">"http://gws.gplates.org/reconstruct/static_polygons/?time=182&model=GOLONKA"</span><span class="w">
</span><span class="n">toarcian_coastlines</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="n">rgdal</span><span class="o">::</span><span class="n">readOGR</span><span class="p">(</span><span class="n">coastline_gws_url</span><span class="p">)</span><span class="w">
</span><span class="n">toarcian_polygons</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="n">rgdal</span><span class="o">::</span><span class="n">readOGR</span><span class="p">(</span><span class="n">polygons_gws_url</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>
<p><a href="https://www.gplates.org">GPlates</a> is software built to reconstruct
palaeogeography using models of continent trajectories through time. By default
GPlates uses reconstructions from Matthews <em>et al.</em> (2016), but it can
interpolate between known continental configurations. This means that you can
get the positions of the continents at any time in the past and export this into
a format for R. This makes the GPlates software useful for producing
reconstructions of several times or producing animations. The web service may be
more time-consuming, having to download lots of data, or restrict you if you try
to grab too much too quickly.</p>
<p>Incidentally, ‘GOLONKA’ in the URLs above refers to the Golonka (2007) model of
continental movement (Vérard 2019).</p>
<h3 id="plotting-the-map">Plotting the map</h3>
<p>To plot the map data, I found that using ggplot is the most convenient as
this provides the <code class="language-plaintext highlighter-rouge">geom_map</code> function exactly for this purpose. I modified the
following code from the gplatesr vignette to plot the base map, ready to add
points later.</p>
<p>Here, I use <code class="language-plaintext highlighter-rouge">geom_map</code> twice: first to add the position of the continental
regions in grey, then to overlay outlines of the modern coastlines. The extra
<code class="language-plaintext highlighter-rouge">geom_rect</code>, <code class="language-plaintext highlighter-rouge">coord_map</code> and <code class="language-plaintext highlighter-rouge">theme_map</code> lines change the look to make the map a
little more appealing.</p>
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">library</span><span class="p">(</span><span class="n">broom</span><span class="p">)</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">ggplot2</span><span class="p">)</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">ggthemes</span><span class="p">)</span><span class="w">
</span><span class="n">toarcian_coastlines</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="n">broom</span><span class="o">::</span><span class="n">tidy</span><span class="p">(</span><span class="n">toarcian_coastlines</span><span class="p">)</span><span class="w">
</span><span class="n">toarcian_polygons</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="n">broom</span><span class="o">::</span><span class="n">tidy</span><span class="p">(</span><span class="n">toarcian_polygons</span><span class="p">)</span><span class="w">
</span><span class="n">toarcian_map</span><span class="w"> </span><span class="o"><-</span><span class="w">
</span><span class="n">ggplot</span><span class="p">()</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">geom_map</span><span class="p">(</span><span class="w">
</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">toarcian_polygons</span><span class="p">,</span><span class="w"> </span><span class="n">map</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">toarcian_polygons</span><span class="p">,</span><span class="w">
</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">long</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lat</span><span class="p">,</span><span class="w"> </span><span class="n">map_id</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">id</span><span class="p">),</span><span class="w">
</span><span class="n">size</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.15</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"#d8d8d8"</span><span class="w">
</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">geom_map</span><span class="p">(</span><span class="w">
</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">toarcian_coastlines</span><span class="p">,</span><span class="w"> </span><span class="n">map</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">toarcian_coastlines</span><span class="p">,</span><span class="w">
</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">long</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">lat</span><span class="p">,</span><span class="w"> </span><span class="n">map_id</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">id</span><span class="p">),</span><span class="w">
</span><span class="n">size</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.15</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">NA</span><span class="p">,</span><span class="w"> </span><span class="n">colour</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"grey30"</span><span class="w">
</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">geom_rect</span><span class="p">(</span><span class="w">
</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">data.frame</span><span class="p">(</span><span class="n">xmin</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">-180</span><span class="p">,</span><span class="w"> </span><span class="n">xmax</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">180</span><span class="p">,</span><span class="w"> </span><span class="n">ymin</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">-90</span><span class="p">,</span><span class="w"> </span><span class="n">ymax</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">90</span><span class="p">),</span><span class="w">
</span><span class="n">aes</span><span class="p">(</span><span class="n">xmin</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">xmin</span><span class="p">,</span><span class="w"> </span><span class="n">xmax</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">xmax</span><span class="p">,</span><span class="w"> </span><span class="n">ymin</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">ymin</span><span class="p">,</span><span class="w"> </span><span class="n">ymax</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">ymax</span><span class="p">),</span><span class="w">
</span><span class="n">color</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">1</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">NA</span><span class="p">,</span><span class="w"> </span><span class="n">size</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.3</span><span class="w">
</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">coord_map</span><span class="p">(</span><span class="s2">"mollweide"</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">ggthemes</span><span class="o">::</span><span class="n">theme_map</span><span class="p">()</span><span class="w">
</span><span class="n">toarcian_map</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">labs</span><span class="p">(</span><span class="w">
</span><span class="n">title</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"Palaeogeographical map of continental plate (grey) arrangement\nin the Toarcian (182 Ma) with modern coastlines outlined above."</span><span class="w">
</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>
<figure class="">
<img src="/assets/images/toarcian_palaeogeographic_map.svg" alt="Palaeogeographical map of the Toarcian" /><figcaption>
Palaeogeographical map of continental plate (grey) arrangement in the Toarcian (182 Ma) with modern coastlines outlined above.
</figcaption></figure>
<p>It’s a decent map. Aside from a few colour changes, from personal
preference, this should cover most of what we want from a base layer. The early
Toarcian is at the earlier end of the separation of Pangaea – the Atlantic has
only just started to open.</p>
<h3 id="plotting-occurrence-locations">Plotting occurrence locations</h3>
<p>The data downloaded from the PBDB include pre-calculated palaeocoordinates when
using <code class="language-plaintext highlighter-rouge">show=paleoloc</code> in the URL. Conveniently, this is often using GPlates, and
the <em>palaeomodel</em> column shows the origin of this. We can just stick the PBDB data
straight onto our palaeogeographical map. Neat.</p>
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">toarcian_map</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">geom_point</span><span class="p">(</span><span class="w">
</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">occ_toarcian_ichthyosaurs</span><span class="p">,</span><span class="w">
</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">paleolng</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">paleolat</span><span class="p">)</span><span class="w">
</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">labs</span><span class="p">(</span><span class="w">
</span><span class="n">title</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"Palaeogeographical map of ichthyosaur occurrences\nin the Toarcian (182 Ma)."</span><span class="w">
</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>
<figure class="">
<img src="/assets/images/toarcian_ichthyosaurocc_map.svg" alt="Ichthyosaur occurrences in the Toarcian" /><figcaption>
Palaeogeographical map of ichthyosaur occurrences in the Toarcian
(182 Ma).
</figcaption></figure>
<p>Ah … well I was hoping for a little more spread! But it seems that just about
all Toarcian ichthyosaurs come from western Europe. This is not surprising –
most specimens are either from the Posidonia Shale Formation of Germany or the
Yorkshire Lias. And this region was a shallow sea at the time – well suited to
many different marine reptile groups. It’s good to know there are more out there
though, covering France up to Norway apparently.</p>
<p>Separating out different groups is also easy to do using <em>facets.</em> In
this case I separated out the different identification ranks for the
occurrences.</p>
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">toarcian_map</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">geom_point</span><span class="p">(</span><span class="w">
</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">occ_toarcian_ichthyosaurs</span><span class="p">,</span><span class="w">
</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">paleolng</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">paleolat</span><span class="p">)</span><span class="w">
</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">facet_wrap</span><span class="p">(</span><span class="n">vars</span><span class="p">(</span><span class="n">identified_rank</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">theme</span><span class="p">(</span><span class="n">legend.position</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"none"</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
</span><span class="n">labs</span><span class="p">(</span><span class="w">
</span><span class="n">title</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"Palaeogeographic map of ichthyosaur occurrences\nin the Toarcian (182 Ma), separated by identified rank."</span><span class="w">
</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>
<figure class="">
<img src="/assets/images/toarcian_ichthyosaurocc_id_map.svg" alt="Toarcian ichthyosaur occurrences separated by identified rank" /><figcaption>
Palaeogeographical map of ichthyosaur occurrences in the Toarcian (182 Ma) separated by identified rank.
</figcaption></figure>
<h3 id="conclusion">Conclusion</h3>
<p>Hopefully you’ll find these code snippets useful to make a map and add
occurrence palaeolocations to this. I was pleasantly surprised by how readily
available the data are and how easy it is to plot in R. Next I’m looking to
add in maps for multiple times and occurrences of different taxa for a project
that, perhaps surprisingly, doesn’t include ichthyosaurs.</p>
<h3 id="references">References</h3>
<p>Blakey, R. 2008. Gondwana paleogeography from assembly to breakup—a 500 m.y.
odyssey. <i>Special Paper 441: Resolving the Late Paleozoic Ice Age in Time and
Space</i> 441: 1–28. <a href="https://doi.org/10.1130/2008.2441(01)">doi:10.1130/2008.2441(01)</a></p>
<p>Blakey, R. 2014. Library of paleogeography. <a href="https://jan.ucc.nau.edu/~rcb7/">https://jan.ucc.nau.edu/~rcb7/</a></p>
<p>Golonka, J. 2007. Phanerozoic paleoenvironment and paleolithofacies maps:
Mesozoic. <em>Geologia</em> 33: 211–264.</p>
<p>Matthews, K.J., Maloney, K.T., Zahirovic, S., Williams, S.E., Seton, M. and
Müller, R.D. 2016. Global plate boundary evolution and kinematics since the late
Paleozoic. <i>Global and Planetary Change</i> 146: 226–250. <a href="https://doi.org/10.1016/j.gloplacha.2016.10.002">doi:10.1016/j.gloplacha.2016.10.002</a></p>
<p>Moon, B.C. and Kirton, A.M. 2018. Ichthyosaurs of the British Middle and Upper
Jurassic. Part 2, <i>Brachypterygius, Nannopterygius, Macropterygius,</i> and
<i>Taxa Invalida</i>. <i>Monograph of the Palaeontographical Society</i> 172
(650): 85–176.
<a href="https://doi.org/10.1080/02693445.2018.1468139">doi:10.1080/02693445.2018.1468139</a></p>
<p>Vérard, C. 2019. Plate tectonic modelling: review and perspectives. <em>Geological
Magazine</em> 156: 208–241. <a href="https://doi.org/10.1017/S0016756817001030">doi:10.1017/S0016756817001030</a></p>Ben MoonAt the end of last year, I was looking at data from the Palaeobiology Database (PBDB) and wanted to draw a map of where fossils were found. I made such maps for Jurassic ichthyosaurs before, which appeared in Moon & Kirton (2018, Fig. 46). These I made by hand, tracing maps from Blakey (2008, 2014) then overlaying palaeo-positions of various ichthyosaur finds. As I remember, the tracing itself was not too time consuming, but wasn’t the most interesting thing I’ve ever done.The joy of a hairline sans2020-11-21T00:00:00+00:002020-11-21T00:00:00+00:00https://bcmoon.uk/typography/the-joy-of-a-hairline-sans<p>I admire good typography. Both the look and idiosyncrasies of pretty fonts, and their arrangement and use in everything from books through billboards to title cards and the words on your phone or computer screen. Making a font is something I would like to try (or maybe have already started…), but not something to undertake lightly. Creating a successful, nuanced, and beautiful font that people will want to use is skilled professional that most people only notice when it <a href="https://www.reddit.com/r/badtypography/">goes wrong</a>.</p>
<p>This post is an appreciation of hairline sans serif fonts. A thin, ultrathin, or hairline sans is an elegant thing to see heading the page at a large size. Whisper thin columnar forms combining the minimum amount of ink with the maximum amount of impact.</p>
<figure class="">
<img src="/assets/images/hairline_sans.svg" alt="A selection of ultralight and hairline sans serif fonts." /><figcaption>
A selection of ultralight and hairline sans serif fonts.
</figcaption></figure>
<p>At this size too, the geometric – Avenir, Gill Sans, and TT Hoves above – are particularly allowed to sing and show their pointed circular forms. Being based on circles and straight lines gives them a very spacious setting – hence Avenir takes up the whole line. Those fonts more closely based on historical text fonts – Macklin Sans and Lato, for instance – retain their curves and more gentile presence.</p>
<p>Sans serif fonts – without the small flicks at the end of lines – have had centuries of history, but most of their variety came over the last hundred years. That variation came from the interpretations and opinions of their creators. Perhaps surprisingly sans serif fonts have largely tracked their own course, and few are directly related or derived from older serif fonts. Connections have been made between 19th Century ‘modern’ serif and early grotesque fonts – for example, compare Bodoni to Akzidenz Grotesk or Helvetica. Similarly in a type family with complementary serif and sans components created from an underlying harmony.</p>
<p>As a prodigy of the 20th and 21st centuries sans serif fonts have that air of modernity about them. Bedecked upon the New York Subway or the London Underground they are the movers of the proletariat; robust yet essential. In another guise inflicting the height of modernity to the rawest photos and artwork. Yet another sitting in refined pose at a graduation.</p>
<figure class="">
<img src="/assets/images/thesis-2_3-in-avenir.svg" alt="Typesetting some of my thesis in Avenir and Warnock." /><figcaption>
I showed you some of my thesis previously, and because it’s convenient for me here’s a little more. Typeset in Avenir and Warnock. Words from Moon (2016) and extended in Moon (2019).
</figcaption></figure>
<p>I used this a little in my thesis, well a lot – every title; adding sans serif to pick out the headings over the main body text. This is not a unique instance … not by a long shot. A hairline, ultrathin, or thin sans serif font is not always good for this, unless it’s rather large. Even in presentations a hairline is a dangerous thing to those attempting to read. Any poorly lit lecture theatre, meeting room, or Zoom call – which is most in my experience – will not forgive you in the slightest.</p>
<figure class="">
<img src="/assets/images/hairline-slide.svg" alt="Hairline fonts are not a good option for a slide presentation." /><figcaption>
Macklin Sans’ hairline fonts, and many other typfaces too, are not my best choice for a slide presentation. Forgive my use of the Solarized colour scheme.
</figcaption></figure>
<p>Properly used thin fonts provide instant impact and long-lasting enjoyment. Placed where they don’t belong they elicit derision or even mistrust. That is not limited to this exclusive group of fonts, but the elements of typography are vast and frequently subtle. It’s worth the dive if you fancy the plunge. I started some time ago and still have that thrill of new discoveries and wonder at others’ thoughts. This remains very much alive too. New fonts are continuously arriving, exploring new ground, rethinking present ideals, and revisiting past successes. And who knows maybe someday I’ll add my own stone to this tower.</p>
<h2 id="references-and-other-reading">References and other reading</h2>
<p><a href="https://www.bookfinder.com/search/?author=&title=&lang=en&isbn=978-0881792126&submitBtn=Search&destination=gb&currency=GBP&mode=basic&st=sr&ac=qr">Bringhurst, R. 2013 <em>The Elements of Typographic Style.</em> 4th Edition, Hartley & Marks. ISBN: 978-0881792126</a></p>
<p><a href="https://blog.hubspot.com/agency/typography-introduction">Leaning, B. 2015. An introduction to typography for non-designers. HubSpot Blog. Accessed 2020-11-21 at https://blog.hubspot.com/agency/typography-introduction</a></p>
<p>Moon, B.C. 2016. Ichthyosaurs of the British Middle & Upper Jurassic & the Evolution of Ichthyosaurs. PhD thesis, University of Bristol.</p>
<p><a href="https://dx.doi.org/10.1080/14772019.2017.1394922">Moon, B.C. 2019. A new phylogeny of ichthyosaurs (Reptilia: Diapsida). <i>Journal of Systematic Palaeontology</i> 17 (2): 129–155. doi:10.1080/14772019.2017.1394922</a></p>Ben MoonI admire good typography. Both the look and idiosyncrasies of pretty fonts, and their arrangement and use in everything from books through billboards to title cards and the words on your phone or computer screen. Making a font is something I would like to try (or maybe have already started…), but not something to undertake lightly. Creating a successful, nuanced, and beautiful font that people will want to use is skilled professional that most people only notice when it goes wrong.Brunel Sinfonia Lockdown Projects2020-11-09T00:00:00+00:002021-04-12T00:00:00+01:00https://bcmoon.uk/music/brunel-lockdown-projects<p>In my non-working time I’m a musician – playing tuba in a few local orchestras and wind bands, and piano for myself in my room. Of course playing together in groups has not been possible for several months now, but one of Bristol’s amateur orchestras – <a href="https://www.brunelsinfonia.org.uk">Brunel Sinfonia</a> – has been able to organise <em>lockdown projects</em> bringing us together virtually to play some pieces you can see on YouTube. Here are links to a few of these videos.</p>
<h3 id="largo-from-new-world-symphony-antonín-dvořák">Largo from <em>New World Symphony,</em> Antonín Dvořák</h3>
<p><em>Uploaded on 10 April 2021.</em></p>
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<iframe src="https://www.youtube-nocookie.com/embed/wnkYhpww-dM" frameborder="0" webkitallowfullscreen="" mozallowfullscreen="" allowfullscreen=""></iframe>
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<h3 id="love-actually-craig-armstrong-arr-tina-mehta"><em>Love Actually,</em> Craig Armstrong (arr. Tina Mehta)</h3>
<p><em>Uploaded on 22 December 2020.</em></p>
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<iframe src="https://www.youtube-nocookie.com/embed/IZIbF-HM_Lo" frameborder="0" webkitallowfullscreen="" mozallowfullscreen="" allowfullscreen=""></iframe>
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<h3 id="danse-macabre-camille-saint-saëns"><em>Danse Macabre,</em> Camille Saint-Saëns</h3>
<p><em>Uploaded on 31 October 2020.</em></p>
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<h3 id="theme-from-et-john-williams"><em>Theme from ET,</em> John Williams</h3>
<p><em>Uploaded on 31 July 2020.</em></p>
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<p>There are some other videos on the <a href="https://www.youtube.com/channel/UCNhGt1V3rYGOpokNEfX_dOQ">Brunel Sinfonia YouTube page</a> – have a look below to see Elgar’s <em>Serenade for Strings</em> and <em>Nimrod</em> from the <em>Enigma Variations</em> – you won’t see me in either of those, but there are plans afoot for more lockdown projects in the near future.</p>
<h3 id="allegretto-from-serenade-for-strings-edward-elgar-arr-gwyn-seymore">Allegretto from <em>Serenade for Strings,</em> Edward Elgar (arr. Gwyn Seymore)</h3>
<p><em>Uploaded on 28 May 2020.</em></p>
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<h3 id="nimrod-from-enigma-variations-edward-elgar">Nimrod from <em>Enigma Variations,</em> Edward Elgar</h3>
<p><em>Uploaded on 7 May 2020.</em></p>
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</div>Ben MoonIn my non-working time I’m a musician – playing tuba in a few local orchestras and wind bands, and piano for myself in my room. Of course playing together in groups has not been possible for several months now, but one of Bristol’s amateur orchestras – Brunel Sinfonia – has been able to organise lockdown projects bringing us together virtually to play some pieces you can see on YouTube. Here are links to a few of these videos.Some palaeoart that colour my walls2020-05-02T00:00:00+01:002020-05-02T00:00:00+01:00https://bcmoon.uk/palaeontology/palaeoart-in-my-flat<p>At the moment, I, and many others, are spending much time indoors. Here in the
UK, the lockdown is likely to continue for some time, in one form or another,
but I’m lucky enough to have surrounded myself with things to keep my interest
and add welcome colour.</p>
<p>Here is a gallery of some of the palaeoart that I have around my flat. You
might sense the theme of marine reptiles, and ichthyosaurs in particular, which
is surely not surprising. Click through on the thumbnails to see the full
images and I’ve included links to the artists below.</p>
<figure class="third ">
<a href="/assets/images/MWitton-Cartorhynchus-hires.jpg" title="_Cartorhynchus lenticarpus_ walk like an ichthyosauriform by Mark Witton.">
<img src="/assets/images/MWitton-Cartorhynchus-th.jpg" alt="Cartorhynchus by Mark Witton" />
</a>
<a href="/assets/images/MWitton-Ophthalmosaurus-hires.jpg" title="‘_Ophthalmosaurus icenicus_ cruise’ (2019) by Mark Witton.">
<img src="/assets/images/MWitton-Ophthalmosaurus-th.jpg" alt="Ophthalmosaurus icenicus by Mark Witton" />
</a>
<a href="/assets/images/BNicholls-EJ-sea-hires.jpg" title="An Early Jurassic hunting scene by Bob Nicholls.">
<img src="/assets/images/BNicholls-EJ-sea-th.jpg" alt="Hunting the Early Jurassic by Bob Nicholls" />
</a>
<a href="/assets/images/VNHM-poster-hires.jpg" title="A poster of the Virtual Natural History Museum featuring critters from each of the geological periods created by Claire Morley.">
<img src="/assets/images/VNHM-poster-th.jpg" alt="A poster of the Virtual Natural History Museum" />
</a>
<a href="/assets/images/VNHM-CambPerm-hires.jpg" title="Tableau depicting the Cambrian to Permian for the Virtual Natural History Museum by Claire Morley.">
<img src="/assets/images/VNHM-CambPerm-th.jpg" alt="V-NHM tableau of the Cambrian–Permian" />
</a>
<a href="/assets/images/VNHM-TriasRec-hires.jpg" title="Tableau depicting the Triassic to Recent for the the Virtual Natural History Museum by Claire Morley.">
<img src="/assets/images/VNHM-TriasRec-th.jpg" alt="V-NHM tableau of the Triassic–Recent" />
</a>
<a href="/assets/images/clock-hires.jpg" title="My wall clock that I put up on my teal wall.">
<img src="/assets/images/clock-th.jpg" alt="My wall clock" />
</a>
<figcaption>A few of the palaeoart pictures that I have framed and put up in my
flat. Images are by Bob Nicholls, Mark Witton, Claire Morley, and a clock
put up by James and Me. Forgive the reflections from the glass: I took these
photos on a nicely sunny day.
</figcaption>
</figure>
<p>I bought the three paintings at the 2018 PalAss meeting in Bristol, and it took
me about a year to get them framed, but the look great to me, complemented by
coloured mounts.</p>
<p>‘<a href="http://www.markwitton.com/shop/4588356872/cartorhynchus-lenticarpus-walk-like-an-ichthyosauriform/11164779"><em>Cartorhynchus lenticarpus</em>: walk like an
ichthyosauriform</a>’
by <a href="http://www.markwitton.com/home/4552741214">Mark Witton</a> features one of
the earliest known ichthyosaurs, thought to be amphibious. <em>Cartorhynchus</em>
was first described by <a href="https://doi.org/10.1038/nature13866">Motani <em>et al.</em> (2015)</a> as the first of series of Chinese
finds from the Early Triassic of short-snouted, ‘transitional’ early
ichthyosaurs, joined later by <em>Sclerocormus</em> (<a href="https://doi.org/10.1038/srep26232">Jiang <em>et al.</em>
2016</a>).</p>
<p>‘<a href="http://www.markwitton.com/shop/4588356872/ophthalmosaurus-icenicus-cruise-(2019)/10882135"><em>Ophthalmosaurus icenicus</em>
cruise</a>’
also by Mark is particularly close to me because a major part of my
thesis was describing material of <em>Ophthalmosaurus icenicus</em>. Lots of material
has been found throughout the Middle–Late Jurassic making this one of the
best represented ichthyosaurs, although the incomplete specimens meant that
knowledge was difficult to summarise for a long time (<a href="https://doi.org/10.1080/02693445.2016.11963958">Moon & Kirton
2016</a>).</p>
<p>A scene of the Early Jurassic by <a href="http://paleocreations.com/index.php">Bob
Nicholls</a>, unfortunately I can’t remember
the title. Here featuring many different characteristic animals from the Lias
including ammonites and fishes, several ichthyosaurs, pterosaurs, and a large
rhomaleosaur taking over and showing who’s boss. The Lias in south-west England
has produced a huge number of different animals, from insects through to ocean
giants, and perhaps has preserved one of the most complete ancient ecosystems in
the UK.</p>
<p>Three posters from the <a href="https://www.facebook.com/virtualnhm/">Virtual Natural History
Museum</a> have pixel art by <a href="https://www.shimmerwitch.space/">Claire
Morley</a> that depicts scenes from each of the
geological periods of the last 540 million years. The V-NHM is an ongoing
project, but these tableau show some of the critters backed by the
period-colours and matching style to the museum itself. I sponsored the Jurassic
Period, being my favourite of them all.</p>
<p>And finally my feature-wall-clock, backed in teal and about a metre across, so I
always know how late I am…</p>
<h2 id="references">References</h2>
<p>Jiang, D., Motani, R., Huang, J.-D., Tintori, A., Hu, Y.-C., Rieppel, O.C.,
Fraser, N.C., Ji, C., Kelley, N.P., Fu, W. and Zhang, R. 2016. A large aberrant
stem ichthyosauriform indicating early rise and demise of ichthyosauromorphs in
the wake of the end-Permian extinction. <em>Scientific Reports</em> <strong>6</strong>:
26232–26239. doi:<a href="https://doi.org/10.1038/srep26232">10.1038/srep26232</a></p>
<p>Moon, B.C. and Kirton, A.M. 2016. Ichthyosaurs of the British Middle and Upper
Jurassic. Part 1, <em>Ophthalmosaurus</em>. <em>Monograph of the Palaeontographical
Society</em> <strong>170</strong>: 1–84. doi:<a href="https://doi.org/10.1080/02693445.2016.11963958">10.1080/02693445.2016.11963958</a></p>
<p>Motani, R., Jiang, D.-Y., Chen, G., Tintori, A., Rieppel, O., Ji, C. and Huang,
J.-D. 2015. A basal ichthyosauriform with a short snout from the Lower Triassic
of China. <em>Nature</em> <strong>517</strong>: 485–488. doi:<a href="https://doi.org/10.1038/nature13866">10.1038/nature13866</a></p>Ben MoonAt the moment, I, and many others, are spending much time indoors. Here in the UK, the lockdown is likely to continue for some time, in one form or another, but I’m lucky enough to have surrounded myself with things to keep my interest and add welcome colour.Two spaces or not two spaces?2020-04-27T00:00:00+01:002020-04-27T00:00:00+01:00https://bcmoon.uk/typography/two-spaces-or-not-two-spaces<p>I’ve seen
<a href="https://www.theverge.com/2020/4/24/21234170/microsoft-word-two-spaces-period-error-correction-great-space-debate">many</a>
<a href="https://twitter.com/rpancost/status/1253802245784842243?s=20">people</a> notice a
change made to Microsoft Word recently: typing two spaces after a full stop (or
period if you’re so inclined) will now be shown as incorrect, with the dreaded
squiggle beneath it, and may be autocorrected to one space. In the strange way
that unexpected things can do, there has been a lot of passion on the two-space
versus one-space debate … debate may be a gracious way to call it though.</p>
<p>Allow me to sum up that <em>it doesn’t really matter</em>. Particularly now there are
far more important things to think about, but I am thankful for distraction from
that, and I’m sure others are too. I have to thank my partner, James, for the
title. I wanted to use ‘Are two spaces better than one?’.</p>
<p>I want nonetheless to go down the rabbit hole for the arguments one way or the
other: where does one space or two spaces come from?</p>
<p>Amazingly, but, perhaps, unsurprisingly, <a href="https://en.wikipedia.org/wiki/Sentence_spacing">Wikipedia has an
article</a> about this very thing,
because the history goes back farther than just using a keyboard with your
typewriter or computer. And the thing about it is that the space between
sentences changes through history.</p>
<figure class="">
<img src="/assets/images/sentence_spacing.png" alt="Different spaces between sentences." /><figcaption>
Examples with large and small spaces between sentences. On top is
an excerpt from <em>The Origin of Species</em>, Sixth Edition (1872), by Charles
Darwin with a large space between two sentences. Below is from <em>Vie de
David</em>, by Thomé de Gamond, printed in 1826. Images come from Internet
Archive.
</figcaption></figure>
<p>From the earliest movable typesetting up until the middle of the 20th century,
many, perhaps even most, published works used a small space between words and a
larger space between sentences. The size might not be consistent, varying
between double space to a full em space, but there was more space between
sentences than between words. Except in France…</p>
<p>Well, not just in France, but ‘French spacing’ uses the same space between words
and sentences, and this took off especially in the 20th century.</p>
<p>The summary from
<a href="https://en.wikipedia.org/wiki/History_of_sentence_spacing#French_and_English_spacing">Wikipedia</a>
is:</p>
<ul class="notice">
<li><em>French spacing</em> inserted spaces around most punctuation marks, but
single-spaced after sentences, colons, and semicolons.</li>
<li><em>English spacing</em> removed spaces around most punctuation marks, but
double-spaced after sentences, colons, and semicolons.</li>
</ul>
<p>With considerable variation.</p>
<p>Typewriters use monospaced fonts, fonts in which all characters have the same
width, and so look monotonous … or whatever the typographic equivalent is.
Picking out the end of sentences with two spaces <a href="https://creativepro.com/double-space-or-not-double-space/">makes
sense</a> and so was
taught to several generations of typists. I was taught the same when I was at
school, even though I was learning on a computer.</p>
<figure class="">
<img src="/assets/images/typewriter_text.png" alt="Typewriter text is monospaced." /><figcaption>
Typewriter text is monospaced and it became common practice to put
two spaces at the end of sentences to pick this point out over the spaces
between words. This text is set in Source Code Pro.
</figcaption></figure>
<p>Books and magazines, however, were switching to a small space between sentences
and so this started the trend towards single spacing. Influential books on
typography and style started suggesting, or insisting, on consistent spacing
throughout. One space between sentences became the new normal.</p>
<p>Desktop publishing software will typically just typeset the text as you write
it, but typesetting algorithms, such as used by TeX, still have wider spaces
between sentences, so this hasn’t completely disappeared. I write my PhD thesis
using LuaLaTeX, so had this typographical nicety, among many others, included in
that.</p>
<figure class="">
<img src="/assets/images/my_thesis_spacing.png" alt="Sentence spacing in my thesis." /><figcaption>
Sentence spacing in my PhD thesis, which is typeset in Warnock
using LuaLaTeX. TeX includes larger spaces at the ends of sentences too.
</figcaption></figure>
<p>In a roundabout way this can be an example for many things: people don’t like
change, they stick with what they know and were taught, but also that changes
can be forgotten surprisingly quickly. The change from large to small
inter-sentence spacing is a subtle one that happened gradually, but I’ve felt
bigger, sudden changes become ever present quickly too.</p>Ben MoonI’ve seen many people notice a change made to Microsoft Word recently: typing two spaces after a full stop (or period if you’re so inclined) will now be shown as incorrect, with the dreaded squiggle beneath it, and may be autocorrected to one space. In the strange way that unexpected things can do, there has been a lot of passion on the two-space versus one-space debate … debate may be a gracious way to call it though.New Digs2020-01-14T00:00:00+00:002020-01-14T00:00:00+00:00https://bcmoon.uk/ichthyosaurs/new-digs<p>Hi, it’s me again.</p>
<p>I’ve been busy over the past two years with several ichthyosaur and other
related research things. I thought I’d come back to the blog to refresh and
update and have ended up with a whole new website! In for a penny in for
a pound … as the saying goes.</p>
<p>I’ve copied across the posts from my old <em>Ichthyosaurs: a day in the life…</em>, so
that all remains to see what embarrassments I put down in years gone by. I hope
to continue and add to that from my current and future research, and other
day-to-day interests. I’d like to also add posts and guides on the research
methods themselves, but considering how successful I was at regular or
comprehensible posting in my last blog we’ll have to see how well it will go
here.</p>
<p>Suffice to say that this is my new homepage – the home of me. I hope you like
it. Hopefully it will also prove useful for spreading the ‘Word of Ben’ – or
whatever else I want to say. We’ll see what more comes and I hope to have it up
and running well soon.</p>Ben MoonHi, it’s me again.Attenborough and the Sea Dragon2018-01-06T00:00:00+00:002018-01-06T00:00:00+00:00https://bcmoon.uk/ichthyosaurs/attenborough-and-the-sea-dragon<p>Recently, I’ve been involved in a documentary with the BBC: <em>Attenborough
and the Sea Dragon</em> will be broadcast tomorrow evening (Sunday,
7 January 2018) at 8pm on BBC1. Here’s the trailer for the programme:</p>
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<p>This documentary follows the story of a newly discovered ichthyosaur found
near Lyme Regis in Dorset, UK. The collector, Chris Moore, is one of those
lucky people who can spend much time on the beach, so has found many
important fossils over many years. This includes the ichthyosaurs
<em>Leptonectes moorei</em>, which is named after him. I also don’t think
I’ve ever seen him not smiling.</p>
<p>I’ll post a bit about how I became involved in the programme, and some of
the story alongside it, after it airs. I’ve only seen an
earlier cut of the programme itself – at that point the producers, editors,
animators, and many more had done a great job – and am looking forward to
experiencing the final version. Hopefully you’ll enjoy it too.</p>
<p>As a bit of a spoiler, you can see write-ups of two parts that Fiann Smithwick
and Emily Rayfield at the University of Bristol – and myself – contributed to
the programme. These cover Fiann’s <a href="http://www.bbc.co.uk/programmes/articles/ZbNR59NVZMsQLfC2qT5SXk/bringing-the-past-to-life-in-technicolour">discovery of preserved
skin</a> on
the ichthyosaur fossil and determining its colour patterning. And Emily’s and
my <a href="http://www.bbc.co.uk/programmes/articles/3gBPbbRKVJQxRMwYkkPqPGM/big-jaws-big-bite">calculating how powerful the
bite</a>
was of another, larger ichthyosaur that was swimming around at the same time.
The programme website is here: <a href="http://www.bbc.co.uk/programmes/b09m2kgl">http://www.bbc.co.uk/programmes/b09m2kgl</a>.</p>Ben MoonAn introduction to Attenborough and the Sea Dragon.From now on2015-12-17T00:00:00+00:002015-12-17T00:00:00+00:00https://bcmoon.uk/ichthyosaurs/from-now-on<h2 id="ichthyosaurs">Ichthyosaurs</h2>
<p>The great thing is that ichthyosaurs are so awesome: no one feels bad about
spending all their time thinking about them. That’s what I’ve spent my last
four years doing. It will also be what I spend a large part of the next three
years doing.</p>
<p>Certainly that doesn’t mean that ichthyosaurs are the only interesting thing
out there: having the joy of being in such a large research group, there are so
many people doing so many different things in palaeontology. I’m looking
forward to the next three years and also the trials and treats they will bring.</p>
<h2 id="next">Next</h2>
<p>All of that is a prelude to the announcement that that PhD that I started in
2011 is now at its end, in the first instance: there remain only the
corrections and eventual publishing (hopefully) to deal with. And in the
meantime, I’ve only gone and wrangled myself a job! much to my parents
amusement, surprise, and pleasure.</p>
<p>The joy of not having a PhD is that there is no burdening deadline rapidly
approaching where everything becomes do-or-die; no letters threatening to kick
me off the course should I not submit by such and such a date (ahem); no late
nights worrying about all those things that you could do, haven’t done, should
have done, want to do … people say that doing a PhD is one of the most
stressful things you can do in life. Thankfully, I’ve spoken to various
postdocs who say that finding grant money afterwards is much worse, so I have
that to look forward to.</p>
<h2 id="strawberry">Strawberry</h2>
<p>But the great thing about doing a postdoc – and, particularly from my point of
view, doing the postdoc that I’m doing – is that what I am doing next is
a continuation and extension: as part of the continuing <a href="http://www.brlsi.org/museum-collections/jesbi">JESBI</a>
(Jurassic Environment of Strawberry Bank, Ilminster; I don’t know whether it
still has that name) project I’ll be doing more ichthyosaurs anatomy, adding in
some marine crocodilians, then extending to do function studies with a slew of
numerical, engineering-based techniques; all in the spirit of onwards and
upwards. This is alongside the <del>venerable</del> esteemed coalition of Matt
Williams (Bath Royal Literary and Scientific Institute); Mike Benton, Emily
Rayfield, and Jakob Vinther (Bristol); Matt Friedman and PhD student (Oxford),
and Andrew Ross (National Museum of Scotland).</p>
<p>Rather conveniently, this has been summed up recently be several of the above
in an <a href="href="http://jgs.lyellcollection.org/content/early/2015/06/29/jgs2">article</a>,
<a href="https://www.leverhulme.ac.uk/awards-made/awards-focus/exceptional-early-jurassic-fossils-strawberry-bank-somerset">webpage</a>,
and was also presented at the Palaeontological Association Annual Meeting
earlier this week. This is simply an introduction and notice of changes – this
post doesn’t actually say that much.</p>
<p>The important thing is: watch this space…</p>Ben MoonIchthyosaurs