Fifty Years of Microbionecrology: A Review (Part 5)

END NOTES

What’s worse than a zombie apocalypse ending civilization?
A zombie apocalypse not ending civilization.

What’s worse than a zombie apocalypse not ending civilization?
A zombie apocalypse not ending civilization again and again and again…

“Fifty Years of Microbionecrology: A Review” was written in (admittedly somewhat early) celebration of the 50th anniversary of George A. Romero’s first zombie movie, Night of the Living Dead. Basically, I’m pretending that Romero’s movies, plus a few other well known zombie movies inspired by the Romero canon, chronicle real events that took place in the years the movies were released. It bears mentioning that this is in direct contrast to Romero’s vision… For him, there was only one zombie apocalypse, and it existed in an eternal now. For example, 2007’s Diary of the Dead is not a reboot of the franchise, but is meant to be taking place simultaneously with the action in the original Night of the Living Dead — it’s the very same night.

The canonical movies in my fanboy Romeroverse are:

1968 • Night of the Living Dead co-written and directed by George A. Romero
1979 • Dawn of the Dead written and directed by George A. Romero
1985 • Day of the Dead written and directed by George A. Romero, and also Return of the Living Dead
1990 • remake of Night of the Living Dead
2004 • remake of Dawn of the Dead, and also Shaun of the Dead
2005 • Land of the Dead written and directed by George A. Romero
2007 • Diary of the Dead written and directed by George A. Romero
2009 • Survival of the Dead written and directed by George A. Romero
2011 • Juan of the Dead

The main text follows this chronology of zombie outbreaks:

1968 • Night of the Living Dead

1979 • Though Dawn of the Dead is copyright 1978 and premiered overseas that year, its U.S. theatrical release was in 1979, so that’s when the zombies return.

1984-85 • While Return of the Living Dead and Romero’s Day of the Dead were both released in the summer of 1985, the events in Return are dated to the night of July 3, 1984, at the beginning of the film. Thus, I imagine the outbreak that begins in Kentucky in July, 1984, growing to become the zombie apocalypse afflicting Florida in October, 1985.

1989 • Tom Savini’s 1990 remake of Night of the Living Dead contains dialogue in a radio broadcast heard by Tony Todd’s character that references a government press release dated August 23, 1989, so the events in the film must take place on 8/23/89 or shortly thereafter.

1999 • Moscow apartment building outbreaks.

2004-?? • Because Shaun of the Dead and Zack Snyder’s remake of Dawn of the Dead both came out in 2004, that fixes the beginning of the latest, ongoing zombie outbreak. Thus, Diary of the Dead and Survival of the Dead must also take place in 2004, although this does result in some technological anachronisms, most obviously in Survival of the Dead.

2007 • Romero imagined Land of the Dead taking place about three years after the end of the world, so if the zombie apocalypse hit in 2004, that dates the events seen in the movie to 2007.

2011 • Juan of the Dead

2014 • The Ukrainian genocide.

2018 • The present, fifty years after the first zombie apocalypse.

However, I’m a science fiction fan, not a horror fan. That distinction may be obscure to some, but the basic difference between the genres is that sci-fi stories are grounded in science and require explanations for whatever weirdness is driving the plot, while horror stories aren’t and don’t. Though that said, playing around with the boundary between science and the supernatural is an old, well established tradition in both genres. Wherever the line between them may be, I think it’s important to be up front with horror fans while I’m playing in their sandbox and acknowledge that I’m not a member of their tribe.

With the exception of the original Night of the Living Dead, George Romero has clearly made a conscious choice to avoid offering, or even suggesting, either a scientific or a supernatural explanation for the resurrection of the dead in his zombie movies. Given that Night and Return of the Living Dead both feature science-based explanations for zombies, I’m guessing that was John Russo’s hang-up. Romero saw no need to explain how zombies work, not even in the sense of having firm cinematic rules for his zombies — a “zombie bible” — as he understood that doing so would limit his creative options for future films. The unexplainable nature of the undead became a convention of the genre that zombie fans accept. There just is no good explanation for how to reanimate the dead, so don’t even try to go there. And the one time Romero did go there back in 1968 is the one moment when Night of the Living Dead is a cheesy science fiction movie on par with the giant insect fear films of the Cold War instead of the first modern horror movie.

But on the other hand, fans know Romero was always consistent (though never entirely serious) about one scientific detail regarding his zombies: George Romero explained the slow, shuffling walk of the undead by saying that their ankles would break if they ran.

I never bought this. Even if Romero’s reasoning was medically sound, his non-brain-eating zombies don’t seem to feel pain, so they would try to run after their prey, break their ankles, and then hobble around with their feet on sideways. Being a science fan as well as a science fiction fan, I’ve long thought that zombies must have an anaerobic metabolism because their hearts don’t beat, their blood doesn’t flow, and the cells in their bodies aren’t being supplied with oxygen. Because fermenting glucose yields just 1 ATP molecule for every 19 the Krebs cycle could regenerate from that same molecule of sugar, zombies are slow and weak. To me, that was a much more satisfying explanation for the zombie shuffle than a fear of broken ankles, and it also explained why they never tire. And because human brains require a lot of energy to operate, it also explained why zombies are dumb in both senses of the word: if they can’t synthesize enough ATP to run, they certainly can’t synthesize enough ATP to think and speak. Although anaerobic environments tend to be acidic, raising the troubling possibility that zombies’ bones would dissolve, such explanatory power made the “zombies are anaerobic” thesis very attractive, and it’s been parked at the back of my mind for years.

Romero fans may be amused (or appalled) to know that the “three-legged stool” model — a bit of fictional science I make much of in the text — was inspired by George Romero’s famously green and blue zombies from Day of the Dead that were really gray.  That is, all Romero’s zombie extras had on gray makeup to give them a proper pallor, but under different color temperature lights, the gray registered as blue or green on film.  Back then, filmmakers couldn’t digitally correct the color timing in postproduction and give everything a uniform look, so Romero was stuck with it.  Rather than explain it away and affirm that zombies really are gray, after all, I ran with it.

The published papers, real and imagined, referenced in the main text are listed below for your edification and entertainment. If you detect a certain bias towards marine microbiologists, that would be the result of my point of entry into the world of single-celled organisms (it started here • the long version • the short version) and its enduring influence on the results I get from Google Scholar — just as generals are always prepared to fight the last war, Google is always ready to help me search for things I’ve already found. In some sense, the more I use Google, the less useful it becomes.  But on the other hand, every once in a while its algorithms fetch back something I didn’t know I wanted because I didn‘t know it existed.  Yup, that’s a thinker.

Anyway, here are all (I think) the scientific references…

REFERENCES

Adey and Wetzel 1975 is an entirely imaginary paper by two powerhouses within their respective fields who get shout outs here because I’m an aquarium nerd and their work had an impact on me.  Walter H. Adey is a famous marine biologist who invented an algae-based biofilter that was widely adopted by big aquariums to help maintain good water quality in their exhibits, and coral reef aquarium hobbyists have come up with smaller and more fuel efficient models that can be DIYed for use in home aquaria.  Robert G. Wetzel literally wrote the book on lake and river ecosystems — it’s called Limnology: Lake and River Ecosystems — in which he argued that the lowest level of any food web isn’t the plants, but the microscopic heterotrophic detrivores that consume dead organic matter and recycle the nutrients that the plants need to grow.  That kinda blew my mind, and I’ve been obsessing over biogeochemical cycling ever since (…which is why I latched onto the idea of cryptic nutrient cycles).

Amend and Shock 2001 cites “Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria”, a real review pointing out how many metabolic pathways for making ATP have been found in thermophilic bacteria (over 150 at the time of publication).  The basic model of anaerobic and aerobic metabolisms says that an aerobic organism can extract 19 times more energy than an anaerobic organism can from a single molecule of glucose, so realistically, you can’t power a human body anaerobically.  Years ago, the first idea I latched onto to explain how zombies work involved the then-recent discovery that low levels of hydrogen sulfide can cause some animals to go into torpor by shifting their cells to alternate anaerobic metabolic pathways associated with hibernation, and IIRC biochemical remnants of this mechanism still exist in human beings.  The scientists involved idly speculated that if this biochemistry could somehow be reactivated, we could perhaps be put in “suspended animation” like in the movies — meaning that in all likelihood, a human body operating anaerobically wouldn’t be able to do much of anything.

Antonius 1973 cites “New observations on coral destruction in reefs”.

Aravind et al. 1998 references the paper “Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles”, which established that archaea and bacteria swapped genes much more readily billions of years ago, when they weren’t so far removed from their last common ancestor as they are now.

Beis and Newsholme 1975 references "The contents of adenine nucleotides, phosphagens and some glycolytic intermediates in resting muscles from vertebrates and invertebrates", a famous zoology paper that compared ATP synthesis in the major muscles of different animals and insects and found that the level of ATP in resting muscles correlated with the amount of energy individual muscles consumed when in use, so for example the flight muscles of birds and insects have very high levels of ATP, and the reactions involved tend towards chemical equilibrium, meaning that animals don’t have internal ATP economies.  That is, we don’t transport ATP synthesized in resting muscles to supply our biggest, hardest working muscles at times of peak demand (during such times, muscles — including human muscles — can operate anaerobically for short periods of time, producing lactic acid).  The Crabtree and Newsholme papers from 1970 and 1972 were cited in the 1975 paper and helped lay the groundwork for it.

Bell et al. 2015 references the paper “Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon” in which was presented the first tiny scrap of hard evidence pointing to a late Hadean origin for life on Earth.  I totally buy late Hadean biogenesis, so stumbling across this paper while trawling through Google Scholar for references to support “Fifty Years of Microbionecrology” was one of those rare moments of Google magic when the algorithms get it right and something genuinely interesting pops up in your search results, and it had to be referenced in the text.

Beschloss 2014 references an imaginary book by presidential historian Michael Beschloss written as a 50th anniversary retrospective on the neverending War on the Dead, which starts out as a play on the neverending War on Drugs and becomes a play on the neverending War on Terror (…starting with the neverending Cold War, not once in my life has the U.S.A. been free of one neverending war or another, and BTW speaking of name brand historians, 30 years ago Paul Kennedy pointed out that historically, spending too much on the military is always what destroys Great Powers).  Recall that an epidemiological study put Patient Zero in central Pennsylvania about 125 miles east of Pittsburgh in 1963 or 1964 (see Fraser et al. 1977), which is why the 50th anniversary book was published in 2014 instead of 2018.

Booth and Doolittle 2015 references the paper “Eukaryogenesis, how special really?”

Boyer 1985 references the book By the Bomb’s Early Light by Paul Boyer, which had such a memorable title (and was such a good book) that even though it was written by a mild-mannered history professor and not a cynical, chain smoking investigative journalist, I had to reimagine it as a bestselling chronicle of the events leading up to Louisville getting nuked and the first crack in the Nixon administration’s stonewalling.  It can’t be an accident that Return of the Living Dead ends with an atomic bomb detonating at what appears to be just before dawn on July 4, 1984: by the dawn’s early light we see the Bomb bursting in air, not that our flag is still there.  Nor do I think it’s an accident that the clock on the wall of the mortuary says it’s just before midnight when the storm breaks and the rain carries the zombiogenic chemical in the crematorium smoke down into the ground: I suspect the filmmakers were referencing the Doomsday Clock maintained by The Bulletin of the Atomic Scientists, which was at 3 minutes to midnight when the movie was being shot in 1984.  And BTW, if you listen closely to the last lines of dialogue after the fade to black, it sounds like the president was planning to visit Louisville…  Of course, at the time the president was Ronald Reagan, who was considered to be something of an idiot and a warmonger by those who disliked him, which in 1985 included pretty much every teenager in the United States of America if for no other reason than because Reagan had raised the drinking age nationwide from 18 to 21 (…or more accurately, he supported legislation that cut federal highway funding to states where the drinking age was < 21), thereby ending a thriving tradition of epic road trips across state lines that were technically bootlegging and all the more epic for it.  So basically, within the context of the time when Return of the Living Dead was shot and released, the last joke in the movie is that radioactive, brain-eating zombies are going to crack open Ronald Reagan’s empty head as the apocalypse gets underway on the Fourth of July.  Happy birthday, America!  Yeah, that’s how we rolled: Reagan got shot in ’81, and ’85 wasn’t Too Soon.  We liked our satire dark Back In The Day.

Bui et al. 1996, Germot et al. 1996, Horner et al. 1996, and Roger et al. 1996 are all real papers that really did establish that mitochondrial genes were encoded in Trichomonas’ DNA, and therefore its distant ancestors had mitochondria and were fully aerobic, not primitive organisms that operated on an ancient, basal, anaerobic version of the eukaryotic metabolism.

Burke 2011 cites “Bacterial community assembly based on functional genes rather than species”.

Canfield et. al 2010 references “A Cryptic Sulfur Cycle in Oxygen-Minimum–Zone Waters off the Chilean Coast” and namechecks a famous marine microbiologist.

Canfield, Habicht, and Thamdrup 2000 references “The Archaean sulfur cycle and the early history of atmospheric oxygen”.

Canfield, Rosing, and Bjerrum 2006 references “Early anaerobic metabolisms”.

Cardona 2014 references “A fresh look at the evolution and diversification of photochemical reaction centers”, a review paper that does, indeed, examine the roots of oxygenic photosynthesis, though it has nothing to say about it originating in predatory biofilms.  The existence of such predators is fictional science, as is the idea that oxygenic photosynthesis evolved to make a toxin that bacteria used to poison anaerobes and dine on their remains — but it does answer the proverbial evolutionary question, “What good is half a wing?”  During a series of public debates over Charles Darwin’s theory of evolution by natural selection, an opponent of evolution famously scored a rhetorical point by pointing out that if creatures with wings evolved from creatures that didn’t have wings, somewhere along the line there must have been a creature with half a wing, and what good is half a wing?  That is to say, what survival advantage would having half a wing confer?  The answer is that with half a wing (or more accurately, with a pair of half-wings) you can jump a little farther when trying to evade a predator, or even jump out of a tree because you can slow your fall.  Turns out having half a wing confers an appreciable survival advantage.  But the same question applies to oxygenic photosynthesis…  For many years, scientists thought it was invented by the first of the Cyanobacteria, the organisms that oxygenated Earth’s biosphere and are the distant ancestors of the photosynthetic organelles in plants and algae, which were originally endosymbiotic cyanobacteria.  The Cyanobacteria were long conspicuous for having started out possessing not one, but two great biological innovations with which to make their way in the world: linking together photosystem I and photosystem II to achieve the high-powered output necessary to split water into hydrogen and oxygen, and the oxygen evolving complex, which is the place in the cell where water is actually split and oxygen is released.  These appear to be unique evolutionary artifacts — biological one-offs — which makes cyano seem implausible, as one innovation is all any species needs to make good.  And indeed, geological evidence has been found in recent years indicating the presence of small amounts of free oxygen in the ancient biosphere, so the oxygen evolving complex appears to have been invented well before cyanobacteria evolved ~2.5 billion years ago.  But the organisms that had the oxygen evolving complex didn’t have cyano’s linked photosystems…  So why was the oxygen evolving complex in use hundreds of millions of years before its power supply was invented?  What good is half of the biochemical machinery cyanobacteria uses to make hydrogen?  If the oxygen evolving complex first appeared way back when hydrogen was still readily available, perhaps the organism that invented it wanted to make oxygen, not hydrogen.  Making comparatively small amounts of oxygen would be useful to power cryptic nutrient cycles and poison anaerobic archaea and bacteria, and when hydrogen got to be in short supply, cyanobacteria figured out how to power up the oxygen evolving complex to make hydrogen for themselves.  Perversely, cyanobacteria were so good at making hydrogen that they poisoned the entire planet with oxygen, destroying the ecological niche their “half a wing” oxygenic ancestors occupied and driving them into extinction while making Life As We Know It possible on Earth.  Fun with science!

Cooper et al. 2018 is an oblique reference to the Romero canon.  The farmhouse in Night of the Living Dead belonged to the Cooper family, and the offscreen death of a Major Cooper set in motion the events seen in Day of the Dead.  BTW, the CRISPR/Cas9 backstory is meant to suggest that human civilization rose in response to the appearance of the undead 5500 to 8500 years ago, a window encompassing both archeologically plausible dates for the first cities and various supposed dates for the moment of Creation (…and of course if the undead have been a recurring problem for all that time, one can retcon them into any setting using any cultural tradition of the risen dead — fun with history!).  The mention of bog bodies and ritual murders is meant to suggest that the undead were enough of a problem for traditions to have developed for making sure slain undead remained slain, from whence we have inherited folk remedies for the undead such as silver bullets and wooden stakes.  The mention of mass extinctions and organic-walled disaster species is an oblique reference to my interest in dinoflagellates, which look like an organic-walled disaster species made good.

Costerton et al. 1995 references a widely cited review, “Microbial biofilms”, and a well-known microbiologist who was informally known as “the father of biofilms”.  In addition to being a significant scientist, Costerton was a significant educator who taught and mentored a number of microbiologists who went on to make names for themselves (see Stewart and Frank 2008).  In the Romeroverse, I imagine him spending the last 10 or 20 years of his career trying to figure out why zombies get thinner and thinner but don’t ever seem to die for good of starvation until, presumably, they fall apart into a pile of bones.

Crabtree and Newsholme 1970, 1972a, and 1972b see Beis and Newsholme 1975.

Darnton et al. 2004 references the paper “Moving Fluid with Bacterial Carpets” (see Kim and Breuer 2008).

David and Alm 2011 references the paper “Rapid evolutionary innovation during an archaean genetic expansion” which does, indeed, suggest a big evolutionary party was going on 3.25 billion years ago, though this is not known to scientists as the Archaezoic Marine Revolution — that’s a little marine biology joke referencing the Mesozoic Marine Revolution.  The reason for this burst of evolution is unknown, and it could just as easily be connected to the evolution of viruses or a new mechanism for horizontal gene transfer that was, itself, spread around by horizontal gene transfer (…for that matter, viruses may well have evolved from little packets of genes that bacteria sometimes release to facilitate lateral gene transfer).  But on the other hand, it’s known that bacteria share genes most readily with other bacteria living alongside them in the same habitat, so it’s not unreasonable to imagine that the invention of bacterial mats would facilitate the horizontal flow of genetic information and set off a burst of evolution.  And this conveniently ties in with the notion of predatory biofilms and helps flesh out the scientific backstory, which is important because the whole idea here is that zombies aren’t a biological anomaly, let alone the miraculous and foretold rising of the dead, but instead are part of the natural world every bit as much as living human beings are.

de Goeij et al. 2008 references the paper “Major bulk dissolved organic carbon (DOC) removal by encrusting coral reef cavity sponges”.

de Goeij et al. 2013 references the paper “Surviving in a marine desert: the sponge loop retains resources within coral reefs”.  Because I’m an aquarium nerd and a fan of their work, recognition for figuring out that the zombie microbiome evolved from a chronic infection festering deep in the rotting lungs of a dying coal miner goes to a bunch of marine biologists who in reality figured out how sponges, survivors from the dawn of multicellular life that may be immortal and are too weird and ancient not to be intrigued by, fit into the ecology of coral reefs.

Dietrich, Tice, and Newman 2006 references “The co-evolution of life and Earth”, which discusses electron donors bacteria have used in the distant evolutionary past.

Dodge 1969 is an inside joke that’s only funny to me…  In a 1965 paper, “Chromosome structure in the dinoflagellates and the problem of the mesokaryotic cell”, J. D. Dodge proposed that dinoflagellates — a kind of algae, some species of which can be very toxic and some species of which can be helpful symbiotes — were “mesokaryotic” organisms descended from a missing link organism that bridged the gap between prokaryotes and eukaryotes.  Dodge was making a reasonable extrapolation from the fun science fact that dinoflagellates store their DNA in a weird way that’s not quite eukaryotic and not quite prokaryotic, but he was wrong; dinoflagellates, which tend to have ridiculously large genomes for single-celled organisms, apparently store their DNA this way to facilitate integrating new DNA into their own genomes, allowing them to steal and hoard genes from bacteria.  He gets cited here solely for the purpose of amusing myself, as obsessing over dinoflagellates is kinda how I autodidacted my way into imagining a properly modern explanation for zombies.

Embley et al. 2003 references a real review: “Mitochondria and hydrogenosomes are two forms of the same fundamental organelle”.

Feynman and Sagan 1980 references a completely imaginary paper that exists only in the Romeroverse.  Richard Feynman was a highly respected and famously impish physicist who played the bongos and took delight in speaking truth to power: when he was working on the Manhattan Project, he taught himself to pick locks to demonstrate to his military overseers that the filing cabinets they were using to store highly classified documents were trivially easy to unlock, and while serving on the committee investigating the Challenger disaster in the 1980s, he shut down bureaucratic waffling over whether or not the O-rings were the problem by showing up at a press conference with a section of the shuttle’s rubber O-ring that he dunked in a pitcher of ice water for a few minutes to show how stiff and easy to split the rubber became at low temperatures.  The Sagan in “Feynman and Sagan 1980” is, of course, Carl Sagan — who, incidentally, was married to Lynn Margulis in the 1960s and ’70s.

Fiore et al. 2016 references the paper “In-silico analysis and implementation of a multicellular feedback control strategy in a synthetic bacterial consortium”.

Fleischmann and Pons 1989 references “Electrochemically induced nuclear fusion of deuterium”, the wildly hyped and rapidly falsified discovery of tabletop cold fusion.

Fraser et al. 1977 references “Legionnaires’ disease: description of an epidemic of pneumonia”, a famous epidemiology paper published in The New England Journal of Medicine that established the existence of Legionnaires’ Disease following an outbreak of pneumonia of unknown origin at a 1976 American Legion convention in Philadelphia — which, course, is the city that the protagonists of Dawn of the Dead flee in 1979.

Garret and Ducklow 1975 cites “Coral diseases in Bermuda”.

Gibbons et al. 2013 references the paper “Evidence for a persistent microbial seed bank throughout the global ocean”, which pretty well put to rest half of a debate that’s been going on since 1934, when Baas Becking famously asserted of bacteria that, “Everything is everywhere, but the environment selects.”  The process of selection is more complicated (and, oddly, also less complicated…) than environmental pressures, but Dr. Baas Becking was correct that everything is everywhere, at least in the oceans.

Grimes 1968 (and all mentions of Dr. Grimes) references a bit character seen interviewed on TV in the original B&W Night of the Living Dead.  I placed his lab in Pittsburgh because it seemed an appropriate homage to George A. Romero, and since Dr. Grimes is not given a first name in the movie, I named him Franklin as an homage to Frank Grimes from The Simpsons.

Grimes and Logan 1977 references Dr. Grimes from Night of the Living Dead and Dr. Logan from Day of the Dead.  In a commentary included with Survival of the Dead, George Romero said that he wanted to connect the characters from his zombie movies, exploring their backstories and eventual fates as they struggle to survive the zombie apocalypse, but he couldn’t do it because he didn’t own the rights to his first four zombie movies (…yet despite this handicap, Romero managed to retcon it into his last zombie movie, Survival, by casting as the protagonist the same actor who had played a bit character named Brubaker in Land of the Dead, and who showed up again in Diary of the Dead as an unnamed National Guardsman who robs the main characters at gunpoint).  So that’s what this reference is all about: Logan was selected for the underground lab in Day of the Dead because he had worked with the famous Dr. Grimes in the ’70s.  Note that according to my timeline, Logan’s surgical approach was out of favor by the mid-’80s.  Thus, he ends up at a small, improvised lab instead of heading up the research program at one of the government’s nice, new redoubts.  And in my imagination, Sarah ends up stuck in (or under) the boondocks with Logan because she’s an uppity female who won’t school in, and Ted Fisher is exiled because he’s gay and out of the closet during the panic over AIDS — there’s a lot of racism on display in Romero’s movies because he understood that people will act on such feelings in the absence of social controls, so it seems reasonable that there’d be no shortage of misogyny and homophobia during the zombie apocalypse, as well.  BTW, while the need to explain why zombies have bright red, seemingly well oxygenated blood goes back to Tom Savini’s special effects in Dawn and Day, if you pay close attention to the blood that’s shed in Land of the Dead, you’ll see that the living actually have darker blood than the dead.  In the director’s commentary, Romero mentions that one of the changes they had to make in order to get an R rating for Land so the film could go into general release was to darken the blood spatters when people were getting killed.  Apparently, censors have no problem with the undead having bright, arterial blood, while their edicts give the living dark, diseased-looking blood…  That seems way more messed up and potentially psychologically uncomfortable for younger viewers than the other way ’round, but there it is.

Hall-Stoodley, Costerton, and Stoodley 2004 references the review “Bacterial biofilms: from the natural environment to infectious diseases”, which to my surprise actually has the phrase “living fossil” in the abstract.  That was a weird little coincidence from my point of view, as I wrote up the bit about black band disease being a living fossil representing the apex predators of Earth’s ancient prokaryotic biosphere long before I even realized Costerton had to have that citation because he’s “the father of biofilms”, let alone found this paper online.

Hays et al. 2017 references the paper “Synthetic Photosynthetic Consortia Define Interactions Leading to Robustness and Photoproduction”, which has nothing to do with calcifying photosynthetic microbial communities slowly and painfully killing people.

Helliwell, Wheeler, and Smith 2013 references “Widespread decay of vitamin-related pathways: coincidence or consequence?”, which examined the loss of the ability to synthesize vitamins by eukaryotes.

Jenner and Jenner 2001 and 2010 are references to Dr. Mrs. Dr. Edwin Jenner, known to us as TS-19, and her husband.  I cited pretend scientists from The Walking Dead because I didn’t want to make a real scientist responsible for my pretend explanation for the origin of the nucleus, which should not be mistaken for a serious competitor in a crowded field and turns the relationship between host and symbiont on its head.  The general consensus is that rather than the endosymbiotic bacteria dominating their archaean hosts by controlling their hydrogen supply, the archaean must have been the dominant partner in the eukaryogenic symbiosis because its need for hydrogen pushed it to rapidly evolve a permanent relationship, binding the bacteria to their hosts both physically (perhaps the first step in the evolution of the complex inner structures seen in eukaryotic cells) and by stripping away genes the bacteria needed to grow and reproduce independently.  Hence the suggestion that a version in which the endosymbiotes are dominant could be a “failed prototype” of the eukaryotic partnership.

Kim and Breuer 2008 references the paper “Microfluidic Pump Powered by Self-Organizing Bacteria”, which first demonstrated that bacteria could be harnessed to pump fluids through a microfluidic array.  The efficiency of the pump is in large part a function of the diameter of the “pipe” the bacteria are in, so this wouldn’t actually work in real blood vessels or lymphatic channels, but it’s the perfect fictional solution for the enduring and fundamental problem of how zombies, who being dead do not have beating hearts, distribute the nutrients they get from eating people throughout their bodies.  And if you buy into the “zombies are anaerobic” thesis presented here, it also solves the problem of euxinia.

Lake et al. 1984 references the paper “Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes.”

Lartillot and Philippe 2004 references a significant paper entitled “A Bayesian mixture model for across-site heterogeneities in the amino acid replacement process” that improved the algorithms for working out phylogenetic trees — impenetrably obscure to the layman, but important to evolutionary microbiologists.  This reference is a shout out to francophones because if you watch The Walking Dead, you know that when everyone else cracked under the pressure, the French stayed in their labs and thought they were close to figuring it out when their generators ran out of fuel.  Y’know, as a science fiction fan, I genuinely enjoy that episode, but the trip to the CDC at the end of season 1 kinda messed up the logic of season 3, as Andrea was very into Dr. Jenner’s little science lecture but never mentioned TS-19 to Milton or the Governor.  I know PTSD can play tricks with one’s memories, but really, now…

Lederberg and McCray 2001 references the origin of the word “microbiome”, coined by Dr. Joshua Lederberg and first defined in “’Ome Sweet ’Omics - a genealogical treasury of words.”

Levy, Fitzgerald, and Macomb 1976 cites “Changes in intestinal flora of farm personnel after introduction of a tetracycline-supplemented feed on a farm”.

Lindmark and Müller 1973 is a reference to “Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate Tritrichomonas foetus, and its role in pyruvate metabolism”, the landmark paper that established the existence of hydrogenosomes.

Logan and Fisher 1985 (and zombies continuing to feed even after their stomachs have been removed) is a reference to Day of the Dead — Drs. Logan and Fisher are the two male researchers in the movie.  Annoyingly, while Dr. Fisher gets a first name (“Ted”) despite having nothing to do in the entire movie but be worried and get shot in the head, the female scientist who not only survives but is the frickin’ lead character is always called by her first name, Sarah, and the internet says she was never given a last name in any draft of the script.  This means I have no way of referencing her or her work short of using the name from the remake of Day of the Dead, Sarah Bowman, and I’m not going there because “Bowman” is such a totally hacky choice of names (it’s fine for a character who’s in Merry Olde England or stuck on a spaceship with an insane AI or based on somebody who was actually named Bowman, but other than that, it should just be off the table at this point), the remake sucked, and I think the original is underrated.  “Fifty Years of Microbionecrology: A Review” is in essence my favorite scene from every science fiction movie ever made, the scene where Dr. Ah-Yes-I’m-Familiar-With-Your-Work explains what’s going on and gets the Hero’s Journey off to a good start, and while watching George Romero’s pictures, I realized that this scene is missing from zombie movies (…hence “Fifty Years of Microbionecrology”).  This scene is archetypical, literally straight out of Hero With a Thousand Faces, and horror as a genre rests in no small part on flipping its script, often making Dr. Ah-Yes-I’m-Familiar-With-Your-Work a deceiver who misleads the Hero.  In the end, the Hero often fails or can at best eke out a pyrrhic victory, holding the evil at bay without defeating it or alerting others to its presence or closing the door on a sequel.  I think one of the reasons zombies persist in the popular culture is that Romero found another, very modern option: the enlightened one is a fraud who knows nothing the protagonists haven’t already figured out for themselves.  Rather than reflecting a traditional moral order, everyone has to make their own decisions in a world in which all order, moral or otherwise, has collapsed.  In short, the zombie apocalypse is existentialist.  There is no Hero’s Journey, there is no possibility of victory or peace, there is only the endless fight for survival, and our heroes are on their own.  Seems like most zombie movies telegraph this by reducing the shaman character to a television set or radio, but Day of the Dead is actually about the shamans as they struggle with the knowledge of their own ignorance, and their leader Logan, Dr. Ah-Yes-I’m-Familiar-With-Your-Work himself, is going insane.  Indeed, the only character he can connect with is Bub the zombie…  The movie seems to be about humans losing their humanity and Bub regaining his, and the two sides pass each other on opposing trajectories during the climax.  Problem is, a Hero zombie who’s helped to perceive a higher level of reality or reach a higher level of consciousness is at best merely returning to his starting point as a person, and is at worst a vastly more dangerous zombie — a zombie with a gun!  So is Day of the Dead undermining the entire construct of the Hero’s Journey, or is Romero suggesting that becoming a fully realized human being is the true Hero’s Journey that all of us must take?

Lovelock and Margulis 1974 references “Atmospheric homeostasis by and for the biosphere: the Gaia hypothesis”, though Margulis later rejected the Gaia hypothesis when Lovelock took the metaphor too far.  The string of references to books and papers by Lynn Margulis is a very nerdy, very meta joke playing on her famous stubbornness and generally contrarian tendencies.  This aspect of her personality worked in her favor when she was leading the charge for a paradigm shift by bringing the old, discarded theory of symbiogenesis back to light and restoring its credibility in the scientific community, but after the argument went from “Is this right?” to “How does this work?”, she was unable to let go of her mental model of eukaryogenesis even when a better alternative became widely accepted (see Martin and Müller 1998).  Despite public accolades, she came to be considered a bit of a crackpot in the scientific community.

Maldonado 2014 references the paper “Sponge waste that fuels marine oligotrophic food webs: a re-assessment of its origin and nature” (see de Goeij et al. 2013).  This paper showed that coral reefs run on sponge poop, which is especially awesome because nobody really knew that sponges even pooped in the first place, let alone that their poop was ecologically important.

Margulis 1981 references the book Symbiosis in Cell Evolution, in which Margulis really did theorize that bioluminescence evolved as a defense against oxygen toxicity, as the biochemistry involves oxidation reactions and is astoundingly efficient at releasing the energy of these reactions as light, rather than heat.

Margulis 1982 references the first edition of the book Early Life.

Margulis and Bermudes 1985 references “Symbiosis as a mechanism of evolution: status of cell symbiosis theory.”

Margulis and Dolan 2002 references the second edition of the book Early Life.

Margulis and Fester 1991 references the book Symbiosis as a Source of Evolutionary Innovation.

Margulis and Schwarz 1998 references the third edition of the book Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, which was the last edition of that book to be titled “Five Kingdoms” (…though in the Romeroverse it was, of course, “Six Kingdoms”).

Marshall and Warren 1982 references the discovery and first laboratory culture of H. pylori, which (under the name C. pylori) the authors proposed caused peptic ulcers in the 1984 paper “Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration”.  Once upon a time, ulcers were thought to be caused by stress, and long-suffering characters with chronic ulcers were a staple of TV dramas and sitcoms, but that trope vanished in the 1980s when it became clear that ulcers were caused by bacterial infections that could be treated with antibiotics.  This discovery won Marshall and Warren a Nobel Prize in 2005.

Martin and Müller 1998 references “The hydrogen hypothesis for the first eukaryote”, which lays out what is now the most widely accepted theory of eukaryogenesis.

Martin et al. 2001 is a real review entitled “An Overview of Endosymbiotic Models for the Origins of Eukaryotes, Their ATP-Producing Organelles (Mitochondria and Hydrogenosomes), and Their Heterotrophic Lifestyle”.  In eukaryotes, core genes relating to the repair and replication of DNA and the synthesis of RNA and proteins are archaean in origin, and interestingly the genes for structural proteins such as tubulin that eukaryotes use to build up complex internal structures with no analogue in archaea (structures that Lynn Margulis took to be evidence for multiple endosymbiotic events factoring into the origin of eukaryotes) turn out to be archaean in origin, as well, while genes relating to a cell’s metabolism are mostly Alpha-Proteobacterial in origin, reflecting the fact that the host cell in the original eukaryotic symbiosis was archaean and the endosymbiont was an Alpha-Proteobacteria.  The implication of this is that eukaryotes started out with exactly one bacterium’s worth of genetic diversity upon which to build our metabolisms, representing a teeny-tiny fraction of all the prokaryotic metabolic diversity that’s out there.

Mauzerall 2007 references “Oceanic photochemistry and evolution of elements and cofactors in the early stages of the evolution of life”, chapter 2 of The Evolution of Primary Producers in the Sea Falkowski and Knoll eds.

Mee et al. 2014 references “Syntrophic exchange in synthetic microbial communities”

Miller et al. 2002 references “Parallel quorum sensing systems converge to regulate virulence in Vibrio cholerae”, the bacteria that cause cholera.  That thiols (the smell of the undead) cause the dead to rise is on me, as some sort of quorum sensing mechanism triggering the spontaneous formation of undead microbiomes looks like the only way to explain the canonical spontaneous reanimation of the recently deceased, and the quorum signaling molecules must be airborne and detectable at extremely low concentrations to be effective over a wide area.  Though on the other hand, aside from “stenches” being slang for zombies in Land of the Dead, the odor of the undead doesn’t really come up in Romero’s movies — the idea that the undead have a signature smell is a nod to The Walking Dead, as characters in that series occasionally hide in plain sight by smearing themselves with zombie guts.

Molin et al. 2003 references “Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure”.

Nelson et al. 1999 references “Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima”, which examined the genome of one of the oldest known bacterial lineages and found how much archaeal DNA it had and what the archaeal DNA was doing.

Nemergut et al. 2013 cites “Patterns and Processes of Microbial Community Assembly”.

Northington, Chavez-Valdez, and Martin 2011 references “Neuronal Cell Death in Neonatal Hypoxia-Ischemia”, which reviews the types of programmed cell death and notes that they are not distinctly independent modes but instead are interrelated and exist in a continuum, like the colors of the spectrum, such that they can blend with each other and intermediate modes of cell death are commonly observed.

Pauling 1970 references Linus Pauling’s advocacy of very large daily doses of vitamin C to prevent illness in the book Vitamin C and the Common Cold.

Pulliam 1975 references the paper “Diet optimization with nutrient constraints”, which presented a mathematical model for how a predator might adjust its feeding behavior to obtain a nutritionally balanced diet necessary to maintain its good health and informed the development of Optimal Foraging Theory.

Ribeiro and Golding 1998 references “The mosaic nature of the eukaryotic nucleus.”

Ritchie and Smith 1995b references a couple of marine microbiologists who are getting shout outs because I’m an aquarium geek — this particular paper was entitled “Carbon-source utilization patterns of coral-associated marine heterotrophs”.

Rix et al. 2016 references the paper “Coral mucus fuels the sponge loop in warm- and cold-water coral reef ecosystems” (see de Goeij et al. 2013).

Rohwer and Youle 2010 is a reference to the book Coral Reefs in the Microbial Seas describing the DDAM model of competition between corals and algae in a popular science format.  The mental models presented by Rohwer (competition between corals and algae is mediated by competition between their microbiomes) and Wetzel (plants aren’t the bottom of the food chain; the bottom of the food chain is a cryptic trophic level of heterotrophic microscopic detrivores that recycle the nutrients — nitrogen, phosphorus, iron, and so on — that plants eat) inform my understanding of how aquariums work and are largely responsible for my idle fascination with microbiology, which eventually led me to argue that the idea of bacterially-mediated competition can be extended to describe competition between not just corals and algae, but also dinoflagellates on coral reefs (and in coral reef aquariums).  From what I’ve read, I’d bet good money seagrasses are in on it, too.

Root, Fritzell, and Giessman 1988 references a paper entitled “Effects of intensive hunting on white-tailed deer movement” that examined changes in deer behavior in response to being hunted, but in the Romeroverse, of course, the “intensive hunting” they were studying was being done by zombies wandering around in the woods.  Hardcore fans may be amused to know that Romero’s last zombie picture was, fittingly, the last one I saw, and I was kinda panicking the first time I watched it because the plot of Survival of the Dead hinges on a new bit of lore: zombies don’t like to eat animals, only people.  In fact, a zombie riding a horse is freakin’ canon now!!!  The idea that deer overpopulation helps zombies survive, if that’s the right word, in the wild between outbreaks was something I thought of literally on day one and was in “Fifty Years of Microbionecrology” from the start last year (…we all needed an escape from 2016, and this was mine — and then the election happened, and there’s no escape from that).  Happily for me, at the end of the picture, the undead fall upon a horse and demonstrate that they’re not such picky eaters, after all, so I was able to write this off as a shift in behavior that occurs at the start of an outbreak.  A general preference for attacking people rather than animals would make sense because that’s how zombies reproduce, and it becomes heightened as part of their generally more aggressive behavior at the beginning of an outbreak.  While this accommodates the new lore Romero introduced in Survival, the question of how a bunch of residents of the Romeroverse could be uncertain about whether or not zombies will eat animals is a bit of a problem…

Russo 1985 references the movie Return of the Living Dead, which is responsible for inserting talking, brain-eating (and also running, though this is not widely recalled) zombies into the zeitgeist.  I include it in the Romeroverse for three reasons: (1) the genesis of the movie was a script by John A. Russo, George Romero’s co-writer on the original Night of the Living Dead, although Russo had written a straight-ahead zombie movie, not the teen comedy gone horribly right that ultimately ended up in the theaters and spawned an entirely new zombie franchise known, confusingly, by the original “Living Dead” name because Russo ended up with the rights to it when he and Romero parted ways; (2) it’s chronologically convenient to pretend that the zombie outbreak it depicts in Kentucky in 1984 is the beginning of the full-blown zombie apocalypse afflicting Florida in 1985’s Day of the Dead; and (3) the idea of using an alternate history to structure the scientific exposition began with a homemade DVD set I found at a local thrift shop in which some random fan had combined in one case the original Night of the Living Dead, Tom Savini’s 1990 remake, Shaun of the Dead, and Return of the Living Dead (…yeah, that’s right: I still buy DVDs).  In addition to behaving differently, the zombies in Return of the Living Dead aren’t vulnerable to head wounds and remain active even after being dismembered.  To make matters worse the picture has undead butterflies and half an undead dog in it, which are problematic both from a microbiological standpoint and for accommodating them in the Romeroverse, as George Romero never showed us any undead animals (…although he did mention in the director’s commentary for one of his movies that he was thinking about zombie animals, and IIRC there was a scene written for Land of the Dead involving zombie rats that was cut for budgetary reasons, so if he’d been able to line up funding for another movie, who knows?).  But I ignore all this because early on, there’s a conversation about Night of the Living Dead in which a character dismisses the movie as a lie the government forced the filmmakers to tell rather than shooting a docudrama about a real outbreak of zombie-ism that was caused by a chemical spill.  The dialogue allows me to pretend that the filmmakers are trying to telegraph to the audience that they’re the ones being pressured by the government to fictionalize the story so as to soften the blow of the nuclear detonation at the end.  Of course, the notion that the filmmakers behind Return of the Living Dead were forced to change their movie into a zom-com would mean that it must be a movie that exists within the Romeroverse rather than a chronicle of events as they happened…  But that’s just one of many conceptual corners that I’ve had to cut in order to stitch this all together, so don’t overthink it, k?  thx!

Song et al. 2014 references the review “Synthetic microbial consortia: from systematic analysis to construction and applications”.

Sontheimer and Brouns 2017 is an imaginary paper based on idle speculation by the scientists in question that appeared in the Nature article “Five big mysteries about CRISPR’s origins”

Sterner, Elser, and Hessen 1992 is a shout out to Sterner and Elser, whose names are familiar because I’m an aquarium nerd and got hip to ecological stoichiometry a few years ago.  The specific reference is the paper “Stoichiometric relationships among producers, consumers, and nutrient cycling in pelagic ecosystems”.

Stewart and Costerton 2001 references a widely cited review, “Antibiotic resistance of bacteria in biofilms” (see Stewart and Frank 2008).  “The father of biofilms” was very interested in antibiotic resistance, so he gets credited with the idea that bacteria brought the dead back to life as a countermeasure to humanity’s use of antibiotics.  This idea is brought up early in the text as an incorrect hypothesis, and its reappearance and reexamination in light of new evidence later on is meant to illustrate how science often progresses in a nonlinear fashion.

Stewart and Frank 2008 references the review “Physiological heterogeneity in biofilms” — the sequence of Costerton et al. 1995, Stewart and Costerton 2001, Stewart and Frank 2008 is meant to imply cohort replacement and the continuity of the scientific endeavor in general as researchers teach, then work with, and then are replaced by their students.  BTW, the mention of ambush predation by a zombie that’s little more than a mossy skeleton is a reference to the “moss walker” seen in season 4 of The Walking Dead.

Süel et al. 2015 references the paper “Ion channels enable electrical communication in bacterial communities”, which really does establish that bacteria can pass electrical signals from one cell to another using ion channels in their cell walls, much as neurons do, to manage the growth and maintenance of colonies.  There has been a lot of work in recent years on how the gut microbiome interacts with the body and brain, but some sort of basis for a direct electrical connection between bacteria and the brain was the last piece of the puzzle to fall into place, so many thanks to Dr. Süel et al.

Süel et al. 2017 is, at the time of this writing in 2016, an entirely imaginary reference.

Takahashi and Yamanaka 2016 references the review “A decade of transcription factor-mediated reprogramming to pluripotency” and namechecks the authors of Takahashi and Yamanaka 2006, “Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors” and Takahashi et al. 2007, “Induction of pluripotent stem cells from adult human fibroblasts by defined factors”, which were landmark papers introducing techniques for creating pluripotent stem cells from mature, fully differentiated mouse and human cells, respectively (…though nifty for research purposes, these cells proved to be therapeutically useless because the process creates genetically damaged stem cells that may become cancerous; scientists have made progress on this front, but it remains a problem).  For those of you playing along at home, the reason the USSR hits Japan with zombies in 2004 along with England and the U.S. is that there’s a cell phone video in Diary of the Dead in which a Japanese woman says of Tokyo, “Very bad here.”  In the director’s commentary, Romero pointed out that the video wasn’t superimposed in postproduction, but was in fact playing on the cell phone when they shot it.  The scenes of violence and destruction seen on television to establish the global nature of the crisis are all stock footage, but George A. Romero actually wrote dialogue for and filmed the Japanese woman, and it obviously tickled him as a filmmaker to have been able to insert the footage of her as a practical, in-camera effect rather than adding it in post.  I can rationalize writing off the stock footage and associated dialogue as a corner I have to cut to stitch together this crazy quilt, but I decided early on that I couldn’t ignore the lady in Tokyo — her story is canonical and must be accommodated.  On the plus side, because Japan is all but totally dependent on its heavily fortified nuclear reactors after 2004, the station blackout in Fukushima is promptly spotted and rectified after the big earthquake and tsunamis in 2011, so the reactors there don’t melt down in the Romeroverse.  Or if you’re into Kabaneri of the Iron Fortress, maybe they do melt down, after all, and that’s why Japan has weird, glowing zombies that are really hard to kill.

Tice and Lowe 2006 is pretty much a straight-up citation of the paper “The origin of carbonaceous matter in pre-3.0 Ga greentstone terrains: A review and new evidence from the 3.42 Ga Buck Reef Chert”.  There’s recent evidence of stromatolites going back to about 3.7 billion years ago, IIRC, but early calcifying communities suggest syntrophies to me.  And I’m also kind of a fan of Dr. Tice’s work, as reading between the lines of some of his papers, I suspect he believes in Hadean biogenesis and was arguing in favor of it as best he could without actually bringing it up.

Tiptree 2018 is a reference to the pseudonymous author James Tiptree, Jr., who wrote the short story The Psychologist Who Wouldn’t Do Awful Things to Rats.  I didn’t intend for this to be the last citation in the text, but I like that it worked out that way.

Tower Report 1987 references the Senate investigating committee report that accused Reagan administration officials of lying to Congress during the investigation of the Iran-Contra scandal and led to months of televised congressional hearings on the matter, which involved the U.S. secretly selling weapons, ammunition, and spare parts to Iran (because the Iranians were at war with Iraq and had a lot of American military equipment left over from the days of the Shah) and using the profits to fund Nicaraguan rebels after Congress in 1982 forbade the use of money from the Defense Department’s budget to support the CIA’s guerrilla war against the communist government in Nicaragua.  So the Reagan administration sold war materiel to an avowed enemy of the United States for the express purpose of subverting the binding will of Congress (specifically, the Boland Amendment). Though this was certainly a high crime and should have resulted in Reagan’s impeachment, the question of whether it was high treason is a little tricky…  The Constitution only mentions treason in the context of a shooting war, but on the other hand, seizing a country’s embassy and kidnapping its diplomats are overt acts of war.  In any case, Reagan skated because he was popular and there was no smoking gun — nor, following the untimely death of former CIA Director William J. Casey, any prospect of finding one.  In the Romeroverse, the Tower Report led to President Nixon’s impeachment and resignation.

Tuchman 1988 namechecks the historian who saved the world, Barbara Tuchman, whose last book in the Romeroverse was not The First Salute, but rather the inevitable “20 years later” retrospective on the outbreak of ’68.

UK Home Office 2014 references the official report on the 2006 assassination of Alexander Litvinenko in London, “Report from the public inquiry into the death of Alexander Litvinenko” — note that this was actually published in 2016, ten years after Mr. Litvinenko was killed.  In the Romeroverse, Mr. Litvinenko was abducted and returned to the USSR by the KGB in 2004, not murdered by the FSB in 2006, and thus the investigation’s results were published a decade later in 2014, not 2016.

Vellend 2010 cites the paper “Conceptual Synthesis in Community Ecology”, which straightened out a long standing scientific mess and gave biologists of every stripe a basic mental model for how communities of plants, animals, and even bacteria are formed (…the short answer is that niches matter, species don’t, and randomness rules).

Weidenheft, Sternberg, and Doudna 2012 references “RNA-guided genetic silencing systems in bacteria and archaea” and namechecks Jennifer Doudna.

Williams and Embley 2014 references “Archaeal ‘Dark Matter’ and the Origin of Eukaryotes”.

Williams et al. 2013 references “An archaeal origin of eukaryotes supports only two primary domains of life.”

Wilson 1990 references E. O. Wilson’s Pulitzer Prize-winning book The Ants, which of course in the Romeroverse is The Zombies.

Woese 1969 is really just namechecking Carl Woese because he was a scientific rock star, rather than referencing any specific paper by him.  But I guess if I have to pick one, I’ll go with “The Biological Significance of the Genetic Code”, which isn’t scientifically significant but looks to be an effort to convince classically trained biologists (many of whom were employed in teaching positions) of the foundational importance of genetics not just in gross Mendelian terms but to the biochemistry and morphology of an individual cell, which makes it kind of interesting from an historical point of view.

Woese and Fox 1977 is a reference to two very famous papers published in 1977 (“Phylogenetic structure of the prokaryotic domain: the primary kingdoms” and “The concept of cellular evolution”) revealing the existence of the archaea as biologically distinct from bacteria, suggesting the three domain classification system, and examining the implications of this discovery.  The technology that made these insights possible was the first widely used phylogenetic assay, based on a highly conserved gene encoding a snippet of ribosomal DNA called 16S rDNA.  It began the shift from classifying organisms by their observable characteristics to classifying them by their genes.  Modern microbial phylogenies are based on 30-40 genes relating to ribosomes and protein synthesis, including 16S rDNA, that are very resistant to evolutionary changes and being swapped around via horizontal gene transfer because messing with them tends to cause cascading system failures and, sooner or later, death.  But even so, it takes some pretty fancy mathematics to tease out a good signal from billions of years of mutational noise (see Lartillot and Philippe 2004).

Woese, Kandler, and Wheelis 1990 references “Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya.”

Woese 1998 references Carl Woese’s paper “The universal ancestor” in which he presented his ideas about the dawn of life.

Zuckerkandl and Pauling 1964 is a real paper, “Molecules as documents of evolutionary history”, suggesting that closely examining the differences between proteins that do the same job in different organisms will yield insights into the evolutionary relationship between them.  That is, changes to important bits of cellular biochemistry happen slowly precisely because those bits are important, so you mess with them at your peril, and molecules (and the genes that code for them) that change very slowly over time are evolutionary signposts.  Following up on this insight led to the invention of 16S rDNA analysis in the 1970s.  Zuckerkandl and Pauling 1964 gets cited here mostly because Pauling was the butt of a joke about his obsession with vitamin C right at the beginning and deserves a shout out for being a genuine genius who helped formulate some big, important ideas like this one.  But then again, he also famously phoned it in when he was trying to work out the structure of DNA and got it wrong.

In closing…

If you’re a serious fan of George Romero’s zombie movies, I hope you’ll forgive the many corners I had to cut to fit together the science and the fiction.  In particular, my fanboy Romeroverse fails to live up to G.A.R.’s vision for his work: there was only one zombie apocalypse, and it’s taking place right now, and all the characters from all his zombie movies are living and dying and coming back to life concurrently, and that means it’s possible to tie them together and develop stories and backstories for them all.  As a fan, I can’t help but view Romero’s movies as being fixed in time.

If you’re a fan of The Walking Dead, be aware that the word “walkers” is canonical. It’s used in dialogue by both Simon Baker and John Leguizamo at the beginning of Land of the Dead, during the raid that brings the wrath of Big Daddy down upon Pittsburgh.

If you’re from Cleveland, the collapse of the redoubt there is the backstory to a line in Land of the Dead. When John Leguizamo’s character says he might head for Cleveland, the protagonist responds skeptically, “Haven't heard from them in a while.”

If you’re from Galveston, that’s on me. Sorry to burn down your town, but there’s dialogue in a news broadcast in the original Night of the Living Dead that places zombies in Houston and Galveston, and what with the Great Hurricane of 1900 being part of local history…

If you’re a scientist, please don’t take offense at my flippant reimagining of your hard work. Any misinterpretations of the scientific papers or the broader implications of the insights therein are mine, committed either out of necessity while trying to make up a vaguely plausible-sounding science of zombie microbiology, or out of ignorance.

Special thanks to my sister and brother-in-law for permitting me to post “Fifty Years of Micriobionecrology: A Review” as a guest entry on their blog, as I don’t exist on social media beyond a Facebook page intentionally left blank as a form of silent protest (…so you’ll have to e-mail me your complaints, I’m afraid). If that strikes you as odd, I submit that a privately run panopticon where social engineering is encouraged for fun and profit is proving hardly less dangerous to civil society than one run by the state. Exhibit A: President Donald J. Trump.

Thanks also to Forest Rohwer, author of Coral Reefs in the Microbial Seas; James Burke, creator of Connections and The Day the Universe Changed; and Ursula K. LeGuin, author of (among other things) the short story The Author of the Acacia Seeds and Other Extracts from the Journal of the Association of Therolinguistics.

Up with the queen!

Part 1 • 1968-1978: The Lost Decade

Part 2 • 1979-1989: The New Normal

Part 3 • 1990-2003: The False Spring

Part 4 • 2004-Present: Conclusion and Current Research Trends