phylogenetic tree

By nature, humans generally like to share what they know – at least, they like to share parts of what they know. The very form and manner we choose to visualize what we know in a way that can be shared with others says a lot about how we see the world.

Tree of Knowledge

For example, one of my ongoing favorite phylogenetic trees, OneZoom, chooses fractal swirls, branches on the tree of life that rotate into ever smaller tendrils, ever closer detail. To me, this reflects our modern ability to see creatures, objects, energies, that are ever smaller. There’s no end to how small we can go.

But visualizing knowledge in the form of branching plant limbs and trees is nothing new.

The Petroleum Tree (1957), an illustration of petroleum uses.
Via: Slate

There’s a beautiful book out, The Book Of Trees by Manuel Lima, that takes a look at the roots of all these trees.

We pick other illustrations, other approaches, but the tree is an old beloved standard. It’s like we’re hardwired to depict knowledge, any kind of knowledge, in some kind of plant or tree-like form.

Given our roots, and given how important trees are to human life, I suppose it’s only natural. What would our visualisations of knowledge look like if we’d only ever seen desert, or rocks, or shallow pools of water?

Tree of virtues and vices (1121)
Via: Papress

Tree of Life
Image: Tree of Life Web Project

The current phylogenetic tree, which organizes the known types of life into groups that share certain characteristics, may have just gained an extra branch way down near the roots. There are three domains: Archaea, Bacteria, and Eukoryota.

While we are used to hearing about a new species of frog or beetle or plant being discovered, these are usually branches or even twigs far up the Eukaryotic line. And it’s accepted that only a fraction of bacteria, one of the three main branches, have been identified.

So it’s kind of major news that a family has been found that don’t fit anything yet known. French scientists at CNRS, the French national research agency, have found viruses that are massive (massive compared to other known viruses, that is). They are large enough to be seen with a regular light microscope, and have almost twice the number of genomes, a different structure and different physical appearances from that of other known viruses.

Pandoraviruses have a much bigger genome, an atypical shape, and different genes from megaviruses (inset), the next largest viruses known to date.
Credit: IGS – CNRS/AMU; IGS CNRS-AMU/Chantal Abergel Via Science

From the original paper: “Because more than 93% of Pandoraviruses genes resemble nothing known, their origin cannot be traced back to any known cellular lineage…The absence of Pandoravirus-like sequences from the rapidly growing environmental metagenomic databases suggests either that they are rare or that their ecological niche has never been prospected.”

I count it as a good day when a major assumption is expanded or upended by scientific research. I would welcome the Pandoravirus family to the Tree of Life, but congratulations are more appropriate in the other direction. Thank you, researchers, for alerting us to something that has been right under our collective noses.

Science paper – Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes by N. Philippe, M. Legendre, G. Doutre, Y. Couté, O. Poirot, M. Lescot, D. Arslan, V. Seltzer, L. Bertaux, C. Bruley, J. Garin, J-M. Claverie, C. Abergel

Science article – Ever-Bigger Viruses Shake Tree of Life by Elizabeth Pennisi

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