f7d9395c_atings_and_reviews___Gwern_net__Review
[Title] Life in Our Phage World [Author] Forest Rohwer [Rating] ★★★★ [Year] 2014 [Read] 2015/02/10 [Review] 
(~400 pages; 4 hours) Saw a New Yorker article on phages - viruses specialized to prey on bacteria - and it mentioned the book was available; so I downloaded the biggest file and started reading. The world of phages is more than a little scary. They have been evolving for billions of years, their numbers are so vast every writer in this anthology resorts to scientific notation (and when they don’t, the numbers are so unfamiliar they look like typos: “By killing nonillions of Bacteria, they have major effects on global energy and nutrient cycles…”), and their generation time is as low as minutes, making for dizzying amounts of selection pressure and optimization - phages seem to have explored every possible way of attacking, subverting bacteria, replicating faster, compacting and making themselves more efficient, and won every arms-race bacteria started with them. If you think you’ve learned some generalization about phages, the next chapter may disabuse you by covering a phage which breaks that rule; and if it doesn’t, it may describe a back and forth sequence of arms races 4 or 5 steps deep. We learn about eerie dynamics like “kill-the-winner”, how φX174 squeezes several genes in by encoding them as overlapping with other genes (and then it gets spookier: “Even in this extremely small genome of a well-studied phage, two genes are not essential for phage replication in the lab, and thus their function has not been determined.”) or how phages proved DNA encoded genetics and their tools have been appropriated for genetic engineering and cancer research (most recently, the CRISPR proteins, a bacterial anti-phage defense system, have been stolen), or the exotic & dangerous locales phage researchers sometimes travel to in order to collect new phage samples or do clinical trials with phage therapy (India and the former USSR, mostly), or how “temperate” phages invade host bacteria but don’t burst it immediately but set up clever timing mechanisms to determine the best time & place to eat their host, or how phages “choose” whether to extend their “whiskers” / “tails” while floating around hoping to latch on to a bacteria (which is unexpectedly active a thing to do for a virus), or (reminiscent of polymorphic computer viruses) they invent mechanisms to shuffle their genes & vulnerabilities implemented in as few genes/proteins as possible. Not all the facts are intimidating - some of the temperate phages help out their host bacteria by bringing along particularly useful genes like photosynthesis, to undo the damage the phage causes; phages preying on bacteria increase bacterial production because when the phages burst bacteria, the bacteria guts are liberated for other bacteria to eat rather than the bacteria getting hoovered up by an amoeba or hydra or something and the resources being locked away and “lost from the productive surface waters, falling as marine snow to deep ocean communities.” Others are intimidating but in a good way (why do our delicious nutritious moist mucal membranes like our noses not get eaten by bacteria? because there’s an even more incredible density of phages in mucus, 40:1, than out, 10:1). The material is presented engagingly - the vocabulary is a bit specialized but explained as it goes, and one can at least follow many of the articles. Most of the articles are interesting, even, although a few enthuse about aspects of proteins or DNA I can’t follow and some are uninteresting to an outsider (who cares about taxonomy?). The illustrations are worth looking at. I have to note the genomes: phages are such genetic minimalists that a functional overview of the gene-regions of phages are presented before each one, and they are sometimes barely a page.
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