A grand vision ·

The Earth BioGenome Project (EBP) seeks to create a new foundation for biology to drive solutions for preserving biodiversity and sustaining human societies.

PNAS cover — Earth BioGenome Project

An enlightened perspective on our planet

The design represents a genomics perspective on the biodiversity of the Earth.

The basis of the design are the shape of continents. These were taken from the award-winning Authagraph Map, which is a projection that strongly preserves shapes and areas. Wired calls it “not perfect, but close”.

▲ Authagraph map by Hajime Narukawa. Shapes and areas are strongly preserved.

I rearranged the authagraph map to fit the aspect ratio of the cover image (nearly 1:1) and allow for enough room for text on the cover. To make things interesting, I put Antarctica in the center — north is everywhere. Given how the image is constructed (read below), I had to remove some islands. Sorry, Madagascar — you're a star.

▲ Layout of authagraph continents.

Australia has the job of representing all of Oceania, such as Inaccessible Island.

For each continent and ocean, a travelling salesman problem (TSP) was solved to find the shortest (or close to it) path that covers the area. The path joins points that were sampled at a level of detail that I thought would strike a good balance between detail and legibility.

Some continents do not have full coverage by the path &mdsah; some small islands and peninsulas were excluded (or extended). This needed to be done to give room for the ocean path between continents and to avoid situations where the ocean path crossed a landmass. The shortest solution isn't always the most appropriate.

▲ A TSP path for each land mass and ocean.

The number of points visited for each landmass were

  1,575 africa
    848 antarctica
  2,818 asia
    475 australia
    713 europe
  1,674 namerica
 17,354 ocean
    872 samerica
 26,329 ALL

I then smoothed the path using a J-spline curve.

▲ A smoothed J-spline of the TSP path for each land mass and ocean. The original TSP path is shown as a thin line.

The DNA double helix is a trope — let's embrace it.

▲ The smoothed J-spline was used to create a double helix. The parameters for the helix were selected to balance detail with clarity.

And before you start pixel peeping: the helix doesn't have handedness. It's composed of three independent stacked layers: one layer per strand strands and one layer with bonds.

Once the helix was drawn, I added bases as circles and resized to increase visibility while avoiding overlap.

▲ Bases are added to the double helix.

The number of base pairs per area is

              nbp
 australia    596 
    europe    872 
antarctica  1,024
  samerica  1,064
    africa  1,911
  namerica  2,033 
      asia  3,403
     ocean 21,208
           ------
           32,111

I mapped species sequenced as part of the Earth BioGenome Project to the path that corresponded to their habitat location. This was done using a combination of automated searches through the Global Biodiversity Information Facility (GBIF) and manual corrections.

For a given path, the length of the sequence of each species was fixed and depended on the length of the area's double helix and number of species assigned to it.

For example, in Africa we have 1,911 bases to distribute across 87 species, giving us `1911/87-1=20` bases per species. The value is rounded down to the nearest integer and the `-1` term allows for a gap between each sequence.

The ocean area is very large and has relatively few species, so we can have long sequences — 396 bases per species.

              nbp   species  bp_per_species 
 australia    596        71               7  
    europe    872       113               6  
antarctica  1,024         2             511  
  samerica  1,064        93              10  
    africa  1,911        87              20  
  namerica  2,033       182              10  
      asia  3,403       206              15  
     ocean 21,208        52             396  
           ------       ---                  
           32,111       806                  

Any bases left over on the helix were assigned to gaps. Initially, I thought of concatenating the sequences without any gaps. While this would allow me to represent (neglibibly) longer sequences, I was persuaded against this idea (thank you Emma!).

First, the Earth Biogenome sequencing isn't complete (nor will it ever be), so gaps in the sequence are a nice metaphor for this. Second, the gaps offer some hope of actually reading the sequences off for each species. Below is a view of one of the strands with the backbone and base pair locations within gaps shown in magenta.

▲ Distribution of gaps (magenta) in the sequence path. Gaps add up to about 5.5% of the total bases in the design.

In the final figure, the helix backbone in gaps is faded.

▲ The double helix is faded in gaps.

In the final figure, bases are colored by nucleotide (A, T, C, G) and region (land vs ocean).

▲ Bases of the sequence are encoded by colored circles. The first base of the first sequence on a path is indicated by a (hard-to-find) black triangle.

You can download each species's sequence and its location.

Sequences were sampled from the Genbank records starting at the first non-repeated base. This was a quick way to avoid spamming the design with polytails.

For example, the sequence for the Hanuman langur

>PVII010000001.1:1-1000 Semnopithecus entellus isolate BS30 SemEnt_scaffold_0, WGS
AAAAA AAAAA AAAAA AAAAA AAAAA AAATT ATTTT GCTAA GGTCT GAGAA CTCCA GAAGG TGGTG TCGTG
----- ----- ----- ----- ----- ---++ +++++ +++++ +++++ +++++ +++++ +++++ +++++ +++++
                                 ** ***** ***** ***

was sampled by skipping the first 28 bases (A's) and uses the sequence indicated by * above.

The position and sequence for each species is shown below. The first base of the sequence is capitalized and remaining are lowercase. The numeric code below the species name is the taxon, a unique taxonomy ID used by Genbank.

▲ Discover what's where. Shown are the species, taxon (unique taxonomy ID) and sequence for each of the 806 species in the design. Species and taxon labels are placed at the average (x,y) position of its bases. It'll do.

A version of the above without the sequence is shown below.

▲ Discover what's where. Shown are the species name, taxon (unique taxonomy ID) and sequence for each of the 806 species in the design. Species and taxon labels are placed at the average (x,y) position of its bases. It'll do.