Genomics is natural history

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As scientists, we live for those lightbulb moments. I imagine we’re more likely to have these moments if we know more natural history, which lets us piece together fundamental facts about our natural world in a new way.

The gents who figured out natural selection first developed a tangible understanding of variation among individuals in the same species from spending lots of time observing and collecting. In a similar way, we couldn’t sort out antibiotics until we understood how different kinds of microbes are in conflict with one another. The development of vaccines followed an understanding of how people develop immunity after exposure to a pathogen. And the development of PCR involved understanding how and where some creatures have adapted to extremely high temperature environments.

In other words, knowing stuff about things matters.

Who would have imagined that knowing about fungi would develop a fix for life-threatening bacterial infections? Or that microbes living in geysers would facilitate a revolution in molecular biology? Just imagine all of the things that we’ve yet to figure out, and the unexpected avenues that will lead us there.

In the last decade, it’s become possible to know a lot more stuff about plants, animals, and other living things. Sequencing a genome used to be a huge thing of its own, but now that’s becoming pretty straightforward. Now we are figuring out when and where critters are using their genomes, by detecting how these sequences are being transcribed into functional roles.

At a conference last year, I sat through a series of (mostly compelling) talks, by folks working to understand how colonies of social insects are organized. In the end, I’d say the majority of talks ended by saying something along the lines of “Now I know that [my behavior of interest] is associated with genes for [certain kinds of biological functions].” This is what I was thinking at the time:

In a classic sense, natural history is made up of things that we know from doing field biology: where organisms live, what they eat, who eats them, how they reproduce, and so on.

Isn’t knowing genomes — and the circumstances under which genes are transcribed — a form of natural history?

Natural history is, arguably, useful only in it its application. The same argument can be applied to genomics.

The funny thing about natural history is you never really know what’s going to be useful, until it’s useful. Yes, we often do targeted experiments to get information that we need, and that information will be useful. (That’s how I call a lot of my work “experimental natural history,” for what it’s worth.) But a lot of folks don’t give a hoot about natural history unless it’s getting applied in a particular way. Which really limits the potential for solving big problems.

Likewise, while I’m not an expert in genomics, I’ve picked up that the level of serendipity required to make new advances is also substantial. (Take, for example, the story of /CRISPR/Cas9). At lest one thing is obvious to me, in this era of genomics: figuring out sequence and when it is getting used is, fundamentally, a matter of organismal natural history. For example, let’s say that you find out that a certain set of genes gets upregulated when an animal engages in defensive behavior. That’s natural history. Right?

I think this is a useful heuristic. I think some of the best science happening nowadays is coming from talented natural historians who are doing careful experiments that involve field biology and genomics to answer classic questions with novel ideas. These novel ideas come from looking at the biology of these systems from a broad view that comes from understanding natural history, sensu lato.

We’re all looking for mechanisms, and working to understand how generalized these mechanisms are. When we know more about the natural history in the field and of the genome, we increase our capacity to paint a clear picture.

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