The ScienceBlogs Book Club

i-4c45ccae66f485d1c9de7df9476e126c-carl_zimmer.jpgJessica asked if I think viruses are alive. John has given his opinion. I will waffle, but I hope in an interesting way. The hard thing about answering that question is that we’d have to agree on what it means to be alive.

We all have a sense that we know what’s alive and what’s not, but I think that sense is really just an intuition. We use different circuits in our brains for recognizing biological motion, for example, as opposed to the motion of rocks or cars or other dead things. But the trouble comes when we try to turn that intuition into definition. We can see that things that look alive to us–tigers, roses, lobsters–share some things in common. And when we get tools to let us see new things, such as bacteria, we wonder, are they like us–in other words, are they alive? I find it interesting that in the nineteenth century, bacteria seemed to be at the hazy border of life and non-life. They seemed to be featureless bags of protoplasm. That was why the research on E. coli I write about in Microcosm was so astonishing. Down to many fine details, E. coli is a lot like us. Their genes are made of DNA. So are ours. They use a genetic code to read those genes and build corresponding proteins out of amino acids. So do we. There are actually dozens and dozens of different amino acids in nature, but E. coli only uses 20 of them to build proteins. We use a nearly identical set. Nobody would claim that E. coli is not alive anymore, because it is so much like us.

But just making a list of traits shared by us and E. coli is not a good definition of life. All known living things use the same set of amino acids. Or at least they did till some scientists engineered E. coli to use “unnatural” amino acids a few years ago. Are they no longer alive? Perhaps there are just a few basic things that qualify somehting as alive. A lot of people like to put metabolism on that short list–the ability to take in food and turn it into living matter. Some would say viruses are not alive, because they don’t have their own metabolism. The classic picture of a virus is a package of genes that uses a host’s cells to make more packages of genes. Yet some viruses appear to grow and undergo other changes outside their hosts, making this a dubious standard.

I also think it’s a mistake to try to cordon off viruses in some non-living quarantine because they evolve, and their evolution is intertwined with the evolution of their hosts. A sizeable chunk of E. coli’s genome is made up of genes delivered by viruses–many of which are essential to the microbe’s survival. The same goes for all the microbes in the ocean, the soil, and in our bodies. I think now of life as a global matrix of genes, shuttling from node to node and changing over time.

So viruses may or may not be alive, but they are definitely a part of life.

I think it’s better to think about life not in terms of hard definitions, but in terms of rules–ways in which species tend to work, no matter how different they seem superficially. The fact that all living things use 20 amino acids is not part of the definition of life, but it certainly is a rule that applies to all life on Earth outside of laboratories. Some scientists think this rule probably the result of some sort of frozen accident early in the evolution of life, or perhaps natural selection zeroing in on the most efficient or reliable system for building proteins.

In the book I also point out other surprisingly widespread rules of life. Life, for example, is robust. In other words, the ways in which genes interact allows living things to stay stable in a world full of change. E. coli copes with rising and falling temperatures, times of feast and famine–all sorts of change–while maintaining an even keel. Its robustness, like our own, is the result of how its genes are organized, like the parts of an airplane. (That’s why engineers are now helping make sense of E. coli’s genes, using the same tools they might use to build autopilot systems.) But that doesn’t necessarily mean that life started out robust to begin with. In each lineage, robustness was a good long-term strategy.

When I imagine the day when we discover alien life, I wonder about whether aliens will be robust too. I also wonder if they will also obey the rules of Earthly life. E. coli and other microbes are surprisingly social, for example, communicating, cooperating, and sometimes even killing themselves for their fellow microbe. Perhaps to be alive is to be social? And the fact that E. coli ages like we do–as an evolutionary strategy to cope with the inescapable decay of biological molecules–makes me wonder if aliens get old too.

Comments

  1. #1 John S. Wilkins
    June 4, 2008
  2. #2 Miss Cellania
    June 5, 2008

    I used to think viruses were the most confusing, until I read about prions. Where do they fit? Alive or not?

  3. #3 CRM-114
    June 5, 2008

    Like a lot of things, it’s all very simple, unless you look too closely.

    The distinction between living and nonliving is artificial. We invented the categories of living things, and of dead things (erstwhile living things which live no more), and nonliving things (which show no signs of life, never have, and we expect never will).

    For millennia people got away with assuming living things and nonliving things were fundamentally different. In 1828 the synthesis of urea knocked the props out from under ‘organic chemistry’ defining life. In 1939 X-ray studies of the tobacco mosaic virus forming crystals made ‘living’ a less viable concept. (Pun intended.)

    Similarly, we used to know what a gene was, and what a species was. Now, not so much.

    Simple concepts can guide us, but we should not take them too seriously.

  4. #4 Eva
    June 5, 2008

    What about the mimivirus?
    http://en.wikipedia.org/wiki/Mimivirus
    Alive? Not alive? Neither/both of the above?

  5. #5 Sven DiMilo
    June 5, 2008

    Prions? Not. No more than any other protein considered by itself. A biological macromolecule with peculiar and interesting properties, but nothing like alive.

  6. #6 Geoff Arnold
    June 5, 2008

    My favourite quotation on the inevitable relativism of this debate:

    “It will not be humans who witness the demise of the Sun six billion years
    hence: it will be entities as different from us as we are from bacteria.”

    - Sir Martin Rees

  7. #7 Katherine Sharpe
    June 6, 2008

    CRM-114 brings up an interesting point about organic chemistry. I remember reading about how, in the early days of the ’30s and ’40s, organic chemists used to boast that someday, they might be able to synthesize a compound in the lab that would be unquestionably alive. Now I wonder what they meant, exactly.

    Carl seems to bring up three different, but all related, ideas about what it would mean to be alive: life evolves, life changes in response to its surroundings, and living organisms age.

    Are all three true for all the living things we can think of?

    And how about reproduction…do all living things reproduce?

    Finally, what’s a prion?
    :)

  8. #8 Jim Thomerson
    June 6, 2008

    Vitalism all over the place! I don’t think there is any such thing as “life”. There are only things which are alive and others which are not. Life, the noun, is in the group with “soul”, “spirit”, “essence”, and the like. I think, in scientific discourse, living and nonliving are acceptable adjectives, but life, the noun, is not.

  9. #9 Oliver
    June 8, 2008

    There’s a lovely essay on this by Bill Pirie in a volume dedicated to Gowland Hopkins in the 1930s which I write about a little in Eating the Sun:

    In the 1930s [Pirie] became one of the first people to crystallise the Tobacco Mosaic Virus. It was a thought-provoking achievement as well as a technically remarkable one. Something sufficiently alive to infect, subvert and kill the cells of plants was also inert enough to be crystallised like table salt.

    Pirie used an analogy from chemistry to explore the insight that things such as viruses could not be treated as simply “living” or “dead”. The words “acid” and “alkaline”, he pointed out, had once been seen as opposites, but modern chemistry saw them as denoting different levels of a single measurable quantity: acids are rich in hydrogen ions, alkalis poor in them. This raised the possibility that the obviously dead and the obviously alive simply occupied different positions on some sort continuum of elan that was as yet not understood. If so, most of what was interesting to biochemists went on somewhere in the middle of this spectrum, at a point where neither the word “living” nor the word “dead” were of much use. “The words still have a very definite meaning when used by poets, knackers or soldiers,” said Pirie, neatly evoking the professions of life and death, “but little or none when used to describe the phenomena observed in tissue culture, virus research and kinetic studies on interrelated enzyme systems.”

    I think there may be more to it than that, but I also think that when we do get fully defintitional we may find that there’s more than one thing we are talking about here.

  10. #10 Russ Abbott
    June 10, 2008

    I’d like to suggest that a fundamental criterion for being alive is the ability (and need) to extract and use energy from the environment. On that score, I guess viruses and prions are not alive, although someone more knowledgeable about them than I might contradict me.

    The ability to extract and use energy from the environment seems to be fundamental to our sense of what we mean by animation, which seems to be one of the ways we distinguish the living from the non-living.

    Although it may make little sense to argue about definitions, the first definition of “animation” on WordNet.com is:

    animation: life, living, aliveness (the condition of living or the state of being alive)

  11. #11 cet
    January 14, 2009

    thanks you good

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