The virus and the cell

The deeper into evolution you get, the more an uncanny feeling of continuity grows. This is especially true when considering viruses and the origins of life. On some level it is easy to think of a virus as a pre-cell; it is smaller, more compact, in some ways simpler. But without a cell, and without access to the extensive machinery required for replication and release of its progeny, the virus is as dead as a ping pong ball floating through space. So while it’s easy to think of evolution linearly – that over time life has grown more and more complex – I think it more likely that the virus came from us, or whatever we were back then (maybe a simple unicellular prokaryote).

Our cells make virus-like particles all the time – little packets of membrane and genetic information which can be taken up by neighboring cells. These exosomes can go a long way along the spectrum of what we think of as self sustaining or infective. Some are just little blebs of membrane and cytoplasm, harmless and useless. Some contain messenger RNA, which when taken up by a neighboring cell will instruct it to make more of this or that protein. Is it a bridge too far to think one of these messenger packets might have gone rogue, carrying instructions for the hijacking of the next cell, instructions for the endless propagation of self?

When you accept the intertwined nature of our fates, the fossils of viruses start popping up all over our own genome. These artifacts are in every cell in our body – approximately 8% of our genome consists of retroviral DNA, genetic information which was stuck in during some ancient infection and has been passed down generation to generation. There’s the Arc protein found in neurons, which could have been co-opted from an ancient virus to allow for better intracellular signaling. There is the HAP2 protein of sperm, which looks an awful lot like a protein many viruses use to invade cells. This protein is so ancient it is found in all living things that mix up their genetic information through gamete fusion, including plants, animals, and parasites such as malaria’s causative agent, P. falciparum. When you take a step back, the two processes are similar – both the sperm and the virus need to breach a cell, inserting its own DNA. Is it possible that the origins of this process resembled a virus invading a cell, and was only later co-opted for the purposes of genetic mixing?

When you disappear down this rabbit hole, viruses start to feel like extensions of us. They’ve intermingled in our genetic ancestry almost since the beginning, giving and taking some of our best biological innovations. Evolution is a tangled web, affected both by our surrounding environment and by the viruses we’ve caught.

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Quote of the Day

There is no need to be frightened. It is true that some of the creatures are odd, but I find the situation rather heartening than otherwise. It gives one a feeling of confidence to see nature still busy with experiments, still dynamic, and not through or satisfied because a Devonian fish managed to end as a two-legged character with a straw hat. There are other things brewing and growing in the oceanic vat. It pays to know this. It pays to know there is just as much future as past. The only thing that doesn’t pay is to be sure of man’s own part in it.
-Loren Eiseley, The Immense Journey

Writing about Biology

I’ve been held up in my writing because I don’t know how to write about science.

This seems counter intuitive. I’ve been doing science for ten years, easily. That involves writing reports, conveying thoughts and plans, organizing data into manageable bundles. But this has always been for other people in my field, or people that I assume know more about the subject than I do, so the occasional hole in narrative is not rare.

On the other hand, writing science on a blog is a very open ended endeavor. Who am I writing for? Interested undergrads? People with no biology background at all? Myself?

Reading Janna Levin’s How the Universe Got Its Spots over the last few weeks, I’ve been inspired by the way physicists approach complex ideas. Although a lot of physics is unapproachable without an extremely high level of math, physicists have a tradition of “thought experiments” that can be easily utilized to make complex ideas about space and time more graspable. Imagine the speed of light is 25 mph. Imagine you have a twin on a train. Imagine you send a man with a stopwatch and a ruler to the other side of the universe.

It makes me jealous. Why haven’t we, as biologist, learned to talk about our field this way? But when I think of the actual subject to be explained, I realize broad thought experiments aren’t really the way to go about it. In biology we already have our unifying theory: evolution. It’s simple. It’s intuitive. It doesn’t need to be kneaded or morphed in order to be readily understood. The complexity of writing in biology comes from the innate microscopic messiness that has sprouted from millions of years of evolutionary divergence.

When you zoom in up close and personal on, say, DNA repair, you are not looking at a single process with an overlying theory or method – there are many mechanisms that have resulted from convergent and divergent evolution, all with implications which can be used to better understand our world. But in the end, you are looking at a small slice of what evolution has done – a band aide for one of the many problems created by the piecemeal system itself. In most cases, you won’t be able to extrapolate much from understanding this specific subsection, a reality that professors wrestle with every day when writing broader impacts for the NIH. So… In the end, what’s the point of knowing?

I want to know so I can marvel. As my favorite ‘armchair biologist’, Annie Dillard, wrote: “The creator goes off on one wild, specific tangent after another, or millions simultaneously, with an exuberance that would seem unwarranted, and with an abandoned energy sprung from an unfathomable font.” Whatever you feel about the ‘creator’, is it not amazing where we’ve ended up from one source? How wonderful would it be to follow just one of these tangents, just to revel in the specificity?