The Microbe That Took Over My Life

i-4c45ccae66f485d1c9de7df9476e126c-carl_zimmer.jpgTo kick off this book club discussion, I want to explain how I ended up the past couple years obsessing over E. coli. If you don't know much about E. coli, it may sound like a strange thing to do. But the time I spent in this microbe's intellectual company was deeply enlightening.

I came to write Microcosm after having worked on several articles and blog posts that swarmed around the same fundamental question: What does it mean to be alive? This is obviously a very old puzzle, but today scientists are attacking it with a fresh passion.

Astrobiologists hoping to find life on other planets, for example, want to know what they should be looking for. Life on Earth is incredibly uniform, based on DNA, RNA, and proteins. Does that mean life on other worlds also have to be made of these ingredients? Synthetic biologists are helping astrobiologists answer that question by tinkering with Earth-bound organisms to see just how far they can alter life as we know it without killing it.

Meanwhile, other biologists are asking fundamental questions about life as they compare the genomes of hundreds of species. Some rules are emerging about how genes must be organized so that their entire network can run smoothly and stably. Engineers are turning themselves into biologists, applying what they learned from building flight controllers to understanding how living things remain stable in a changing world.

By studying genomes, scientists are also learning some surprising lessons about how life evolves. Along with the flow of genes from ancestors to descendants, they're also finding evidence of a sideways flow--in other words, organisms can slurp up genes from other species. Darwin's tree of life is morphing into something more like a world-wide web. To understand what it means to be alive, we may have to look away from individual creatures and turn our attention to entire ecosystems, entire planets.

As I learned more about all this work, I knew there was a book to be written. But I also knew that unless I found a way to narrow the scope, I would need a trillion pages to finish the job. So I started thinking about how I could find a manageable path through all this science. It was not until I was driving down a desolate stretch of the New Jersey Turnpike, somewhere around Penns Grove, that the solution came to me. (If you ever have writer's block, I suggest taking a trip down that way.)

I would write a biography of E. coli.

For seventy years, this resident of our guts has been poked and prodded by scientists, who have won a dozen or so Nobel Prizes for their efforts. By studying E. coli, scientists figured out some of the most fundamental questions about life--what genes are made of, how they give rise to living matter, how genes change over the course of evolution. When scientists then turned to other species, they found time and again that other organisms followed E. coli's rules. "What is true for E. coli is true for the elephant," the French Nobelist Jacques Monod once famously said.

Today scientists also study many other species, but E. coli remains at the core of research into what it means to be alive. One reason for its popularity is that it was also the first organism scientists discovered how to genetically engineer--in other words, to insert genes from other species into it for fun and profit. Now they're altering E. coli in far more radical ways, turning into, among other things, a living camera.

Some of the rules of life that E. coli can reveal are not rules that some people want to hear about. If you think that every species has some impenetrable integrity that must never be violated, E. coli is going to make you very unhappy. Creationists tried to use E. coli as evidence that life could not have evolved complex traits, but it's got the marks of evolution all over it (including microbial versions of ostrich wings).

So you can see (I hope) why a couple years spent pondering E. coli can be a couple years very well spent. I'm very excited that Scienceblogs has picked Microcosm for its first selection in its book club. I'm a loyal reader of all three of my fellow club members, and I'm very curious to see what they think of the book--which parts spoke to them the most. Of course, I'll also be looking forward to comments people leave here, some of which I'm sure will spur us to new discussions.

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Admission first: I have not had the opportunity to read your book yet. However, I have read quite a bit of The Loom. I am very glad to see this book club come into existence. It's an excellent idea!

You and your comrades here are doing a great service for laypeople like me. Where else could I go to learn so much about current life science studies/discoveries/thoughts/etc., short of enrolling at a university? What guarantee would I have assuring me that my teachers would be so well versed, so articulate, so inspirational? I trust you, because you've shown yourself (as have your compatriots) to be an educator with integrity to match your passion. You help to keep me fascinated, and I am grateful.

I look forward to getting your book. Based on all I've read on your blog I know it will be worth far more than the asking price.

in other words, organisms can slurp up genes from other species.

Isn't it more like genes can sometimes be so tenacious and promiscuous, so viral, that they sometimes jump into other species?

I read Lynn Margulis' Acquiring Genomes a while back (I think I need to re-read it again before understanding some of the more complex parts). Some of the stuff in there looked a bit flakey and tenuous, but after learning that a huge chunk of the Wolbachia genome had been found embedded in fruit fly genomes, the ideas in that book suddenly started looking a lot more on-target.

Definitely interesting stuff going on...

By Owlmirror (not verified) on 04 Jun 2008 #permalink

What I find interesting is the idea that there is no more a distinct "line" between living and non-living and the discussions on this book club have been confirming my view that life is a gradient. I don't think that we will ever have a definition that accurately describes the difference between pre--biotic and biotic organisms.

Carl, you mention the implications for astrobiology, and I think that it also has implications for understanding abiogenesis as well. It seems to me plausible that abiogenesis was never a singular "event" in earth's history, but a process that has been going on for 3.5 billion years under our noses.

I think it entirely possible that once the process of RNA/DNA replication took hold in the pre-biotic world (or even PNA for that matter) life may have started in multiple locations around the planet. I have heard my abiogensis theorists claim that it had to be a singular event, but I am not clear on how they are so certain about it. My visualization of abiogenesis resembles a color strop with fine gradients between hues.

On the lower frequency end of the strop, the colors are clearly dominated by red hues. As the frequencies increase towards the other end of the strip, one can pick a distinct yellow, green, blue or violet group. Finding a discrete point at which green turns to blue, blue to violet is nearly impossible. Supposing that each pixel along the strop represents a separate hue, adjacent hues will be different however the differences will be so minor that the threshhold of difference is too slight for human perception.

And yet, red is clearly different from orange, orange sifferent from yellow and red is nothing like violet.

Can abiogeneisis be a continual process that has been proceeding in fits and starts for 3.5 billion years? I don't know, but considering a paper recently published by the Harvard Medical School, I certainly think it is a possiblility.

I have your book on order from Amazon, thanks to this book club discussion!