Science Ruins Science Fiction Again

Last month, Russian researchers struck frozen science gold--an ancient lake, buried deep under the Antarctic ice sheet. Given that Lake Vostok had been isolated for probably millions of years, the Russians were under a lot of pressure (just like the lake! because it's under a really heavy ice sheet, get it?) to protect this unspoilt environment from contamination.

But what about the possibility of contaminating ourselves with stuff from the lake? As my brother pointed out,

While this is undoubtedly an exciting moment for science, all I can think of is a science fiction story in which a bacterium discovered in a place like this causes a worldwide pandemic.

To which I replied: okay, fun concept, but totally unrealistic. Then we got to talking about parasitism and co-evolution and . . . well, let's start at the beginning.

As soon as you move into another organism, you're a symbiont. Symbionts can be beneficial or harmful; the harmful kind are called parasites. So, bacteria that live in people and make them sick are technically a kind of parasite--though people often say "parasites and bacteria" the way they used to say "animals and fish." (Yes, fish are technically and in all other ways animals.)

Now, all symbiotic relationships are products of co-evolution. The parasite evolves to survive inside the host, while the host evolves to reduce the harm done by the parasite. (There are a lot of strategies for that, by the way--from making initial infection more difficult to quarantining, expelling or killing the parasite). As the host environment becomes more hostile, the parasite evolves clever coping mechanisms, and so on.

Because of the specificity of most parasite-host relationships, it's highly improbable that a parasite could survive for millions of years without its host*. And if it did survive, it would probably do so by evolving  into such a different form that it couldn't re-infect its old host.

That's why I'm pretty confident there aren't any nasty little parasitic bacteria in Lake Vostok, waiting to pounce on us.

Okay (said my brother) but why couldn't a non-parasitic Vostokian bacterium initiate a pandemic as soon as it was exposed to people? Every relationship has to start somewhere, right?

Sure, a free-living bacterium that had never encountered humans before could theoretically find its way into an unsuspecting scientist (poor Dr. Lukin!), survive long enough to reproduce, and start a new symbiotic relationship. But the environments of Lake Vostok and the human body are radically different. A bacterium (or any other critter) is much more likely to move inside an organism if that organism's internal decor is similar to the environment it's already adapted to. The 37 °C of the human body would almost certainly kill bacteria adapted to the -3 °C of Lake Vostok.

~Tangential Musing On Evolutionary Timescales~

Even if a brand new bacterium entered a human and survived, we'd probably never know about it. As a general rule, it takes a long time for symbioses to evolve, and it's very hard to study them when they're just getting started.

Imagine a cafe full of college freshman--there's probably a lot of flirting, but none of it may ever turn into a relationship. Tracking all the potential interactions, most of which will be dead ends, would be a huge challenge. Now consider that plenty of pairs of college freshman are likely to hit it off with each other, but most biological interactions that could become symbioses are nipped in the bud when one organism kills the other.

How long would it take to evolve the sort of traits that make for a proper pandemic? I don't know, but I wonder if anyone's done any theoretical modeling of this . . .

~End Tangent~

All the really scary epidemics in human history have come about through jumps between similar environments.

Human to human is the most obvious--Europeans bringing syphilis to the New World, for example. We often use the term "first contact" to refer to the meeting of colonizers with natives, which is a bit misleading, since we also use that term in science fiction to refer to the meeting of humans and aliens. The former is fraught with peril of disease; the latter, not so much.

Humans around the globe belong to the same species and are similar enough to fall prey to the same parasites. But in most speculative cases, humans and aliens belong not only to different species, but to entirely different evolutionary histories, perhaps going back to the origins of life itself. The idea of a parasite, carefully co-evolved with its host, being able to jump across such a gap as that--well, it strains my imaginer.

But what about zoonoses? Aren't those examples of parasites jumping suddenly from one host species to another? Well, yes and no. Many parasites have co-evolved with both human and animal hosts, and require both to survive. Malaria is carried by mosquitoes, but can't complete its life cycle without humans. Other zoonotic parasites, like Toxoplasma, are stuck in an evolutionary dead end if they accidentally infect a human--they can survive but not reproduce.

The zoonoses that truly "jump" from species to species, successfully infecting and propagating through their new host, always move between similar environments. Ebola can only infect primates. Even versatile diseases like West Nile virus are restricted to vertebrates--a tiny fraction of the world's animal diversity. There's no way you're going to "catch" colony collapse disorder from a bee, or bitter crab disease from a crab.

So, let me sum up.

Likely sources of pandemics: "first contact" between groups of humans that have been isolated from each other; places where humans and other vertebrates live in close, unsanitary quarters.

Unlikely sources of pandemics: Lake Vostok, Mars.



* Modern humans (Homo sapiens) weren't even around when Lake Vostok was last connected to the rest of the world, but there were definitely early hominids.

Sorry I Don't Have A Lab

I just received a most curious missive: an application for a postdoctoral position in my laboratory! The sender wrote seven careful paragraphs about their* research experience and attached their CV.

It is not spam--the person is a legimitate researcher with published papers and all that jazz. But I rather suspect it is the machine-gun approach--the same e-mail sprayed liberally across a field of potential hirers.

What could possibly have tipped me off? Well, a wee bit of judicious googling might have informed the applicant that I am currently a freelance writer and therefore unlikely to be looking for postdocs. And there's no mention anywhere of how their interests and research experience makes them a good match for my laboratory. Instead, I read this:

After the six years of study and nearly two years of work experience on biology, my work covered from cell biology to molecular biology, from cell manipulation level to gene clone and shut down. I'm confident that I can be competent to most of biological work.

Whoa! Whoa. Just, whoa. A purely cellular and molecular background means you've only half-experienced the field of biology.

I know, because my predominantly ecological and evolutionary background has left me in the same situation. When I read about the work this applicant has done with DAPI fluorescent staining and monoclonal anti-α tubulins and dsRNA interference, those are just words to me. I've never used those techniques.

But have they ever had to use the weather and season and time of day to guess where they'd find their study organism? Have they ever sampled quadrats along a transect line? Or spent hours just sitting still and watching animals? These are the techniques of the ecologist--dare I say the naturalist?--and they are just as much a part of biological work as ultramicromorphological observations.

Should the applicant ever engage in the aforementioned judicious googling and stumble across this blog, I would like to thank them for giving me an excuse to jump on my soapbox and whine about the rift between mol/cell and eco/evo. I've been here before, lamenting the negative stereotypes each side entertains about the other:

Mole/cell biologists are narrow-minded, technique-obsessed fly-counters and yeast-spreaders, driven by medical funding, with no interest in the big picture and no grasp of how life works in the real world. Meanwhile, eco/evo biologists are tree-hugging, touchy-feely, pot-smoking hippies who failed chemistry and use science as an excuse to hike in the rainforest and dive in the tropics.

Mmmm, diving in the tropics . . . oh wait. Actually, despite my background, I'm not eco/evo. I didn't do a single quadrat or transect for my thesis. In fact, I spent my PhD years in a little-known third camp, a track that Stanford calls Integrative/Organismal, or I/O.

My dissertation was indeed extremely integrative, if you take "integrative" as a fancy word for "all over the map."

I had a chapter of genetics. A chapter of biomechanics. A chapter of oceanography. A chapter of in vitro development. And an appendix of almost straight natural history. My thesis had ADD, and that probably counts as a win for the I/O track.

But I/O is still the narrowest slice of biology at Stanford. There are only two active I/O faculty, compared to twenty-three mol/cell and eighteen eco/evo. And those two guys have been around for a while. I never heard any murmurs of hiring into I/O, and I rather suspect it will die out when they retire.

And that's too bad. I really liked the idea of a third camp that straddled the line, spanned the divide, crossed the tracks. I wanted it to stimulate collaboration and mutual understanding. If I had my own laboratory, that's what I would do with it. Instead of hiring "I'm confident that I
can be competent to most of biological work," I would look for "I'm eager to broaden my molecular and cellular background into ecological and evolutionary studies."

But that's if I had a lab.

If I had a lab
I'd integrate in the morning
I'd integrate in the evening
All over the seas
I'd integrate questions
I'd integrate techniques
I'd integrate love between mol/cell and eco/evo
All over this land


* I am using singular they, as I am uncertain of the sender's gender. "But you are a grammar snob!" I hear you protest. "How can you condone singular they?" All I can say is this: it's the worst solution to the problem, except for all the others.

run, microbe, run!

The field of microbiology is incredibly exciting and has way too many words for the things it professes to study. More on those words in a moment! Let us first attempt to describe microbiology in the most general terms. "Micro" just means "small" (or, if you want to be precise, 10^-6), but microbiology is not merely the study of small things. It is the study of microscopic things, things too small to be seen with the unclothed eye. Of course, individual human cells are (mostly) microscopic, but studying them is cell biology, not microbiology. So, let us qualify further: microbiology is the study of whole organisms that are microscopic. That still leaves us a mind-boggling array of study organisms:

animals
plants
fungi
bacteria
archaea
viruses

Heck, that's just about every kind of life you've ever heard of (and maybe one kind you haven't, unless you've been reading). Wait a sec--are viruses organisms? Well, most viruses are bacteriophages (yum, yum, bacteria!) and they have a pretty notable impact on bacterial populations, so just from that perspective, it seems like folks that study bacteria ought to care about them.

Now let's get back to those "too many words," because they get thrown around all the time. Some of this terminology is taxonomically outdated, but it sticks around due to a combination of practicality and linguistic inertia.

Microbe is the most general term, and it includes--you guessed it--all microscopic organisms. Eukaryotic microbes are all called protists although they have very little in common with each other; they include the protozoa (similar to animals), algae (similar to plants) and (similar to fungi)*. Prokaryotic microbes include the domains Bacteria and Archaea, which, like protists, are only superficially similar to one another.

I really wanted to sort all that out, but actually the only microbes I'm going to talk about are bacteria. Marine bacteria, to be specific, because the coolest stuff is always in the ocean.

However, as cool as the ocean is, it is also a very difficult environment to study, and thus the field of marine microbiology is only a few decades old. We've only just begun to characterize the diverse** microbial fauna of the seas. So, most of our knowledge of detailed bacterial behavior comes from the bacterial poster child: Escherichia coli. It's big, it's easy to culture, and it's everywhere. It uses flagella (powered by nature's only true rotary motor) to swim around. Different species of bacteria can have any number and distribution of flagella.

E. coli have peritrichous flagella, which they use to swim with a strategy called "run and tumble". The bacterium wraps all of its flagella up into one propeller, swims in one direction for a little while, then suddenly flings the flagella apart, which halts its progress and reorients it in a random direction. Rinse and repeat. If you want to explore a given area for tasty things, this is a pretty decent way to do it; it's more or less a random walk.

Marine bacteria, on the other hand, exhibit a different behavior, called "run and reverse". It's just what it sounds like: swim in one direction, then turn around and swim back. This sounds like a great way to get nowhere fast, but wait! Marine bacteria are tiny. Much tinier than our friend Escherichia. They are so tiny that the Brownian motion of water molecules becomes relevant to them, and they end up constantly bombarded with H₂O. So whatever direction they think they're going in, they'll almost certainly be headed off in another direction. In this context, the run and reverse strategy is totally reasonable.

To conclude, I present a mindblowing calculation from Fuhrman (Nature, 10 June 1999). Quick background: He's talking about two weird ways that microorganisms could pick up genes their parents didn't give them. Viral nonspecific horizontal gene transfer is when a virus picks up DNA from one host and transfers it to another, totally unrelated host. Natural transformation is when organisms pick up "loose" DNA dissolved in seawater and incorporate it into their own DNA.

Now. Take a second to let your mind recover from contemplating these bizarre possibilities, then read on . . .

"Although transfers of these sorts may be extremely rare, the typical bacterial abundance of 10⁹ per litre in the euphotic zone and the huge volume of the sea (3.6 X 10⁷ km³ in the top 100 m), coupled with generation times on the order of a day, implies that an event with a probability of only 10^-20 per generation would be occurring about a million times per day."

Wow.




* I've always been kind of annoyed that there isn't a separate word for the fungus-like protists. But they make up for it by including the ultra-sci-fi slime molds in this group.

** How diverse can it be? you ask. They're tiny! They're single cells!

But ah! I respond. The many faces of diversity! What microbes lack in morphological diversity, they make up in metabolic diversity.

one-eyed cows of the sea

I'm not talking about the romantic sea cow, morphologically named, but the ubiquitious sea cow, ecologically named.

Shame on me for using such fancy words! I meant this: copepods are sometimes called the cows of the sea, not because they look anything at all like cows (they don't) but because of their somewhat bovine behavior. They are herbivores--grazers of phytoplankton--and they are very good at it. The fact that all of the carbon, photosynthetically fixed from carbon dioxide into useable sugars by tiny single-celled oceanic grass, is available to be transported on up the food chain to eventually build tuna and whales, is due in large part to the steady, efficient grazing of copepods.

But, as I said, they don't look anything like cows. They are small (millimeters) and crunchy (exoskeleton). The stereotypical copepod has long, sweeping antennae and one eye. A single eye. In the middle of its head.

For a long time that didn't seem too weird to me, any more than anything else in the routinely weird and wacky world of biology; it was just something to remember about copepods--like a rhinocerous having horns. But just recently, as I sat in class watching a professor draw a copepod on the board, I automatically corrected him when he drew two eyes--and it struck me, quite suddenly, that the cyclopsian nature of the copepod is totally and utterly bizarre.

Let's take a moment to talk about bilateral symmetry. It's another biological fact that we tend to take for granted--that if you drew a line down your middle, the left side would roughly match the right. It's by no means a rule of life--think of anemones and jellyfish, who display radial symmetry, or sea stars and urchins, who've taken it a step further to pentaradial symmetry.* But bilateral symmetry has been around for a pretty long time. The most primitive bilateral animals are the flatworms, and they have two eyes even though they don't have a coelom**.

So I started reading up on copepods, and I found out that the single eye of adult copepods is a "persistent" larval feature. Like most other aquatic crunchies (crustaceans), copepods have a larval stage called a nauplius. It looks rather simpler than the adult forms, and with successive molts it adds appendages and segments until it has the proper number to be considered a grown-up. The nauplius form is also simplified by having a single "median" eye--that is, an eye that is set nicely in the center of its head (like a cyclops) and not off to one side (like a pirate).

Most copepod nauplii simply retain this median eye as they mature into adult forms, but most other crustacean nauplii (and a few copepods) split their eye up into the two (or more) compound eyes of adults. At least, that's what we think happens, but this hypothesis has not received unanimous support, so I suppose some folks think that the adult eyes derive from some entirely separate tissue.

I haven't found any explicit evolutionary discussion of this phenomenon. I can only suppose, however, that the single eye of the nauplius is a derived character. That is, I expect that crustaceans evolved from a two-eyed ancestor, and as their larvae became more and more specialized, some developmental gene mutated and they ended up with only one eye.

I'd welcome any discussion, wild hypotheses, or research articles on the subject. Be warned, however, that searching for the words "copepod" and "eye" together yields a wealth of information about the very intimate relationships many copepods have with the eyes of other organisms. What I said about copepods as grazers is all very true, but the group has diversified incredibly, and they have also excelled at the parasitic lifestyle.



* Actually, echinoderms are weird when it comes to symmetry. Their larvae are actually bilaterally symmetrical, and it is only when they settle and turn into adults that they develop radial symmetry. Bilateral symmetry is partially preserved in the sea cucumbers, and it is actually one of the characters that makes echinoderms close cousins to chordates. Read more!

** A coelom is a body cavity, the hollow bit inside you that holds all your gooey organs; since they don't have a coelom, flatworms are just solid chunks of tissue. Being a solid chunk of tissue, they can't have circulatory systems or respiratory systems, and have to rely on diffusion to move gases and nutrients around their body. Relying on diffusion means you need a really large surface area to volume ratio, and it's this restriction that keeps flatworms flat. I used to be rather disdainful of the flatworms for being acoelomate; after all, the flatworm representative we meet most commonly in the lab, Planaria, is kind of cute but doesn't have much to recommend it. But then I met the marine flatworms, some of whom are more spectacular than nudibranchs, and I opened my mind to acoel virtues.

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The cyclopsian nature of the copepod is a deep mystery of evolution. Even flatworms have two eyes. (I used to be rather distainful of the acoels, until I met marine platyhelminthes--some are more spectacular than nudibranchs.) Photosensors came before bilateral symmetry? Who was the first crustacean? I can only assume that whoever he was, he had two eyes, and the one-eyed character of copepods is a derived one. Even flatfish don't lose their lower eye, but bring it around to the other side.

I've no time to research this at the moment, but soon.