The Virus That Learns

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If you don’t have an immune system, you don’t last long in this parasite-riddled world. Your body receives a steady stream of invaders–viruses, bacteria, and other pathogens–which it has to recognize and fight. In many cases, it’s a brutal battle with an ultimate goal of eradication. In other cases, the immune system simply keeps strangers in check, preventing them from spreading. As many as a third of all humans have cysts in their brains containing a single-celled parasite called Toxoplasma. As long as the parasite stays in its cyst, the immune system lets it be. If Toxoplasma breaks out and starts to multiply, however, the immune system picks off the new cells. And if people lose their immune system–due to HIV infection, for example–Toxoplasma runs rampant and causes devastating brain damage.

The cells and molecules we use to recognize these invaders are unquestionably amazing. What’s perhaps most amazing is that the immune system can learn. When a new pathogen turns up, our immune cells undergo a kind of interior version of natural selection. Over the course of several cell divisions, new variants emerge that do a better and better job of recognizing the newcomer. Our bodies can then mount a powerful, focused attack on, say, a particular strain of the flu. And once the immune system learns how to recognize that new enemy, it can store that memory away, enabling it to attack the same pathogen years later.

This is the sort of thing that people often have in mind when they refer to us as a “higher” form of life, and bacteria and viruses as a “lower” form. Bacteria are just simple individual cells. They’re not multicellular organisms that can dedicate billions of cells to making antibodies, spewing poisons, and carrying out the many other tasks required for an immune system to work. Viruses–forget about it–they’re just protein shells that package a few genes, which they insert into a host cell.

But the higher/lower dichotomy is a blinkered way to look at life. If you can’t believe that bacteria can have an immune system, then you will miss the clues that they, in fact, have one. And the evidence is overwhelming.

Bacteria, after all, live in the same parasite-riddled world as we do. They may not get infected by the same pathogens that infect us, but they are continually hounded by viruses. A microbe that can defend itself against a virus will have a huge edge in the evolutionary race against its fellow microbes.

The threat of viruses has driven the evolution of some pretty impressive defenses. Bacteria make enzymes that lock onto certain, short sequences of DNA and slice them apart. When a virus injects its genes, these so-called restriction enzymes shred them into genetic confetti, so that they can’t take over the cell.

Written By: Carl Zimmer
continue to source article at phenomena.nationalgeographic.com

6 COMMENTS

  1. One nice throwaway comment in the article is “Maybe Lamarck would have been better off as a microbiologist.” Because of the power of the basic tenets of Darwinian theory, we often scornfully dismiss Lamarck’s notion of organisms passing on to their offspring characteristics they acquire in life. I vividly remember a school biology teacher summing up Lamarck: “According to his theory, everyone who has a wooden leg gives birth to babies with wooden legs.” But the fact is that in the microbial world, it is entirely possible for cells to pick up genetic information or undergo genetic changes that are inherited by their progeny.

    Carl Zimmer’s beautifully written article describes viruses and bacteria pinching DNA barcodes from each other during the process of invasion, then passing on the newly acquired sequences to their offspring. But this is by no means the only example of Lamackian inherit among microbes. Most of the spread of antibiotic resistance among bacteria is the result of horizontal gene transfer, not point mutation. Viral lysogeny could be regarded as a temporary setting for Lamarckian inheritance. Events such as gene duplication and chromosomal reassortment occur during the lifetome of existing cells, with the results passed on to the lineage. (Everybody’s favourite yeast species, Saccharomyces cerevisiae, belongs to a group of related single-celled fungi with an ancestor that duplicated all eight of its chromosomes!).

    I’m emphasizing these examples of the essence of Lamarckism partly because I get fed up with creatards and even some who should know better (most recently Brian Cox in his Life TV series) who seem to think all evolution arises from point mutations to DNA. Remember Richard Dawkins’ famous encounter with a fundie camera team asking how information can be increased by mutation? It’s not just microbes that acquire foreign DNA. Mammalian genomes show clear evidence of acquisition of DNA from viruses, too. Natural selection is happy to work its effects on changes in DNA, however they’re acquired.

    • In reply to #1 by FrankMill:

      One nice throwaway comment in the article is “Maybe Lamarck would have been better off as a microbiologist.” Because of the power of the basic tenets of Darwinian theory, we often scornfully dismiss Lamarck’s notion of organisms passing on to their offspring characteristics they acquire in life. I vividly remember a school biology teacher summing up Lamarck: “According to his theory, everyone who has a wooden leg gives birth to babies with wooden legs.” But the fact is that in the microbial world, it is entirely possible for cells to pick up genetic information or undergo genetic changes that are inherited by their progeny.

      You don’t appear to understand Lamarkism. What you’ve just described are mutations of genes, chromosomes, and genomes, not actual acquired characteristics. To prove Lamarkism, you’d have to show that a phenotype like a polypeptide could reverse-transcribe as a stretch of DNA or RNA, which then goes back into the genome so that its copies can create that phenotype over. For macroscopic organisms with complex embryologies, you’d have to show that the genome acted like a blueprint that corresponded piece-by-piece to pieces of the finished organism, and posit a feedback mechanism by which a phenotypic change in the organism could change the corresponding part of the genome. Nothing in your comment even comes close to accomplishing any of this.

  2. Bacteriaphages are the future of antibiotics. It’s an old Soviet technology that never came to the West because of petty cultural problems. I was hoping for some mention of that, but I learned so much from this terribly interesting article I’m not complaining. It expanded my appreciation for Darwinian design. This site rocks.

  3. [edited to add; in reply to Zeuglodon]

    Point taken. Strict Lamarckism is indeed as you describe it, and both I and the author of the microbe immunity piece have fallen for the watered down version of the term, referring to inheritance of DNA encoding traits acquired during a cell’s lifetime.

    I think you’re stretching the meaning of the word “mutation” by including large-scale events like gene and whole chromosome duplication, but the word we really need to clear things up is an adjective; “random”. Creationists love to scorn that the theory of evolution hinges entirely on chance mutations. They don’t understand that natural selection is a non-random process that works statistically to favour or disfavour the random changes. My point (and Carl Zimmer’s) is that there are many examples in which what Zeuglodon terms a mutation arises as a result of an adaptation made directly in response to a situation confronting a cell’s survival. Such non-random mutation is, I agree, not Lamarckism in its strict, original sense, but it results in a similar outcome.

    • In reply to #5 by FrankMill:

      [edited to add; in reply to Zeuglodon]

      Point taken. Strict Lamarckism is indeed as you describe it, and both I and the author of the microbe immunity piece have fallen for the watered down version of the term, referring to inheritance of DNA encoding traits acquired during a cell’s lifetime.

      I think it would be more helpful simply to drop the term altogether. Lamarckism is based on two categorical principles: use and disuse; the inheritance of acquired characteristics. Use and disuse states that a pre-existing adaptation that is used will improve in some way. The principle could only cover the crudest improvements, is solely based on facts about physiology that themselves need to be explained (why do muscles grow stronger when exercised, for example, instead of atrophying?), and is utterly powerless to explain organized complexity such as the eye and the brain. The inheritance of acquired characteristics is solely about phenotypic characteristics. Acquired genes or genetic mutations are another matter entirely, and fall under the umbrella of genetic mutation.

      I think you’re stretching the meaning of the word “mutation” by including large-scale events like gene and whole chromosome duplication,

      A mutation is a change in the structure of a gene or set of genes that makes it or them different from a copy of the pre-mutated gene or genes, whether by a nucleotide changing or by duplication of stretches of DNA. I got this point from actually studying how geneticists classify mutations, so it’s no idiosyncrasy of mine. There’s no difference in principle between a small-scale mutation and a large-scale one beyond how much of the genome changes, so unless you think genomes aren’t sets of genes, I don’t see how it’s “stretching” in any way. If anything, I’d suggest your assumption that a mutation has to be small is unjustified and based on a limited stereotype of the concept.

      but the word we really need to clear things up is an adjective; “random”. Creationists love to scorn that the theory of evolution hinges entirely on chance mutations. They don’t understand that natural selection is a non-random process that works statistically to favour or disfavour the random changes.

      Agreed, but the argument was a red herring in the first place. It doesn’t make a blind difference to natural selection whether the variation offered up was random or not, so long as the differences between them improved or worsened their respective survival and reproductive successes.

      My point (and Carl Zimmer’s) is that there are many examples in which what Zeuglodon terms a mutation arises as a result of an adaptation made directly in response to a situation confronting a cell’s survival.

      Name an example of such an adaptation, if you’d be so kind. The one that comes most readily to mind is the exchange of genetic material between bacterial cells, and that has nothing to do with cells promoting their own survival. The beneficiary of such adaptations has to be the genes, so if it is advantageous to design machinery that allows them to jump ship, the genes will design cells that enable them to jump from one cell to another. Not only that, but under conditions such as unstable environments, genes can form coalitions that are mutually beneficial, or parasitize another organism’s or cell’s adaptations for their own benefit.

      Untangling your claim, your causal arrow looks like this:

      Cell survival threatened (causes) => adaptation to be made directly in response (causes) => mutation to arise

      Firstly, where does that newly-made adaptation come from? Secondly, how does that adaptation reverse-transcribe into genetic material, and after this show that the new genes code for that phenotype in later generations? Thirdly, how do you distinguish the example from the Baldwin Effect, in which an environmental pressure repeated over generations on a conditional strategy creates an evolutionary pressure for innate or non-conditional strategies in response? I raise the last point in particular because claims of Lamarckism often turn out to be the Baldwin Effect.

      Such non-random mutation is, I agree, not Lamarckism in its strict, original sense, but it results in a similar outcome.

      Non-random mutation is just that: non-random mutation. Unless that mutation was the result of an acquired phenotype reverse-transcribing into the DNA or RNA of a genome, calling it Lamarckian is unjustified.

      I think you’d do well simply to drop the term Lamarckism altogether. It’ll only lead to confusion, and there’s no need to redefine a term that already has such unhelpful connotations attached to it.

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