Evolution up close at a distance

We have met the tangled bank, and it is us

We’re in the midst of an evolutionary event—a speciation event. I write this with neither awe nor relish. For what that means, for the virus and for us, is messy, many-sided, up close and at a distance; you need to turn the telescope both ways to get at it.

Nextstrain is an open-science effort to track and document the genomes of pathogens. The group has compiled data on a menagerie of disease-producing pathogens—au courant critters like CoVid-19 and Zika, and ancient fellow-travelers like Dengue, Measles, and Tuberculosis. With CoVid-19, they’re capturing genetic sequencing as from incoming test samples, mapping the emerging strains as they appear around the world.

Above: screenshot of phylogenetic tree compiled by Nextstrain, showing 2434 sampled genomes, rooted to early samples from Wuhan; there are other ways of visualizing these data. Screenshots used under a CC-BY-4.0 license with thanks to nextstrain.org.

And yes, that plural is correct: we’re dealing not with one, but multiple strains; the virus is changing as the pandemic unfolds. Nextstrain is tracking these strains as mutations crop up in samples gathered from around the world, cobbling them together into a living phylogenetic tree.

What’s striking to me about Nextstrain is the way the project apprehends the crazy-making scalar unwieldiness of molecular evolution—and the patchy, nebulous, dappled way it presents itself in evidence. Dependent on the vagaries of testing, which vary enormously (and disastrously, as we’ve seen in the US), these data emerge in shreds. As their writing makes clear, Nextstrain’s resulting maps are inferential and hypothetical. They’re good at showing their work, though, making explicit both the underlying messiness of viral phenomena and the rule-of-thumb quality of working assumptions. The “temporal resolution” of their phylogenetic tree, they disclose, “assumes a nucleotide substitution rate of 8 × 10^-4 subs per site per year.” Interestingly, this order of magnitude, implying change on the scales of thousands of years, also has been used to model the evolution of the coronaviruses as a group, resulting in a model that has them emerging within the last 10,000 years. (It’s important to note that Nextstrain ventures no inferences about the deep-time evolutionary history of the pathogens they track.)

Recently, it’s been argued that the messiness of mutation and substitution in the coronaviruses implies a much deeper evolutionary history. A 2013 paper that tries to model the undulating complexity of evolutionary change employs “evolutionary models that account for variation in the pressure of natural selection across sites in viral loci and lineages”; which imply “that coronaviruses are orders of magnitude older than suggested by previous molecular clock analyses.” In this view, the coronavirus is a strange stranger, a fellow traveler accompanying the lineages of mammals and birds since they diverged. The story of viruses is a kinship story.

Are these deep-time rates of change commensurable with the assumptions that shape the CoVid-19 phyologenies at Nextstrain? Possibly (and I’d love to talk to molecular biologists about this): as the Nexstrain folks aver, “there is considerable uncertainty surrounding estimates of transmission dates and in reconstruction of geographic spread.” It’s also important to note that the changes cropping up in test samples aren’t necessarily functional—molecular mechanisms exist to “correct” these changes, and there will be selective pressure to knock them down over time.

We are right now living in evolution; something unfolding over millions of years is present to us right now, manifesting all its dark abundance. We have been taught to marvel at the scale of natural selection—a thing which, we are told, unfolds over geologic time. Only here, it is also present to us, in febrile, sticky intimacy. What seemed an insensible entity, accruing remotely and abstractly over millions of years, can also obtrude with vivid intimacy, also can make time seem to stop. This is a story of kinship, of entanglement, of the uncanny mingling of temporal scales, of the ways in which life on earth is always close up at a distance.

There is a lesson in all this about climate change, too.

Selective fitness, alas, is no guarantee against misery. And yet, we will survive—the virus wants us to survive.

Although, as Randall Munroe points out, they may not be enthusiastic about the ways we have of surviving:

Above via xkcd.com under a Creative Commons Attribution-NonCommercial 2.5 License.