Tuesday, March 8, 2016
Shakespeare, Rome and Paul Revere — the networks
This blog has emphasized that phylogenetic networks are fundamentally different from other types of biological network. For most networks, the nodes and the edges are observed — the nodes represent objects (organisms, proteins, species, etc), and the edges represent known interactions between the objects (so that they are sometimes called interaction networks).
For phylogenetic networks, on the other hand, the leaf nodes are observed while most of the internal nodes are inferred (except perhaps in population studies) and all of the edges are inferred. These networks rarely make it into books with "biological networks" in the title.
That does not make interaction networks uninteresting, of course. Indeed, they can be an excellent way of summarizing complex data. Below, I illustrate three examples from the humanities, just to emphasize how different they are from phylogenetic networks.
The first example is from Martin Grandjean's blog. You can download the full-size network poster from there. What the networks show is the structure of Shakespeare’s tragedies — I have chosen the play Macbeath for illustration. Two characters are connected in each network every time they appear in the same scene. The Network Density is a measures of how complete is the network (ie. all possible edges between its nodes). As you can see, Macbeth himself is at the centre of several poorly connected groups of people in the play.
The second example is from the Moovel Lab web page. You can check out the interactive graphic there. What the network shows is all of the roads that lead to Rome (ie. the shortest road route to Rome from any given point in Europe or Asia Minor). You will note that it is basically tree-like, as expected, but the sea routes form reticulations.
The third example is from Kieran Healy's blog. You can read the full explanation there. It concerns the historical figure Paul Revere, who was involved in the American Revolution. The fable tells us that he rode through the night calling out "The British are coming", but for a number of simple reasons this must be pure poppycock. The following network shows you what was his real role. There were a number of groups of people who banded together to ignite the revolution, and the members of these groups are connected pairwise in the network. The network is very clustered, indicating that these groups had few members in common. If you look closely, you will see that Paul Revere was the only person involved in all of the groups. This makes him a far more important person that history has credited him.
I think that interaction networks are fun, as well as informative.