Humans are less human than we thought.
September 13, 2012 3:37 AM   Subscribe

Icky face-pooping flesh mites are only the tip of the iceberg. You've heard that your gut bacteria are necessary to help you digest, meaning not all germs are bad. Without them, we couldn't digest healthily. But stop and look at how far our interconnectedness with other forms of life goes: 1. Human DNA itself is at least 8.3% ancient viruses; without one of these viruses you could never have been born. 2. Mitochondria in human cells originated when the same type of bacteria that causes typhus disease raided one of our cellular ancestors and instead of hijacking it was pressed into service. (The same origin as chloroplasts in plants from cyanobacteria). 3. Far more of the cells in your body are non-human microorganisms than actual human cells. This relationship is not just interconnectedness. This is integration.

This post was inspired by a recent post about Demodex Folliculorum.

4. There has been a reported case of a bacterium acquiring some of our DNA in the aforementioned manner, though it might have just been sample contamination.

With the completion this year of both the ENCODE project (previously) and the human microbiome project, it's possible that information from one might lead to insights into the other.

Life is fractal: We're complex individuals who are part of a complex society that's part of a complex species that's part of a complex biosphere. Threads in the tapestry of life. We're also tapestries ourselves: We are the universe for trillions of smaller organisms. Each of the Earth's 7 billion-plus human bodies contains about ten times more microorganism cells than human cells.

Turns out, human biology is a lot like an old article in The Onion:
World's Top Scientists Ponder: What If The Whole Universe Is, Like, One Huge Atom? ....Among the revolutionary ideas expected to be raised at the historic week-long summit is the possibility that, like, our whole friggin' universe might be just one big atom in, say, some super-duper huge thing out there somewhere, or something. ...."Even weirder is, like, if we're just one big atom in a larger universe, how do we know all the little atoms don't have, you know, little universes in them, with, like, little people living on them, with little cars and little houses, and maybe even itsy-bitsy tiny-ass international symposiums on cutting-edge theoretical physics, even."

The relationships between different organisms sharing a body is either symbiotic, commensal, parasitic, or pathogenic.

Just as some microorganisms maintain symbiotic relationships with us, their hosts, we might someday find a way to be more symbiotic with the global biosphere of which we're a part. Before our host planet recognizes us as a pathogen.
posted by Sleeper (59 comments total) 96 users marked this as a favorite

life is gross
posted by ryanrs at 3:43 AM on September 13, 2012 [11 favorites]

This post is amazing.
posted by molecicco at 4:05 AM on September 13, 2012 [1 favorite]

Goddamn, we're awesome and gross.
posted by Pope Guilty at 4:09 AM on September 13, 2012 [10 favorites]

Thanks, I'll skip breakfast.
posted by Brandon Blatcher at 4:14 AM on September 13, 2012 [1 favorite]

Between this and the news about how we might just simulated, I'm pretty much losing my will to do anything other than dream and contemplate my icky, icky, neural networked non-human navel.
posted by knile at 4:17 AM on September 13, 2012 [1 favorite]

If we were computer simulations, you'd think we'd show some signs of intelligent design, instead of all this mess with viruses and goo and invisibly tiny lobsters nibbling our eyelashes.
posted by Sing Or Swim at 4:20 AM on September 13, 2012

If we were computer simulations, you'd think we'd show some signs of intelligent design...

Depends on the level we are simulated at. And, for that matter, the goals of the simulation. "Could you make life work with a mess of viruses and goo? Let's simulate and find out!"
posted by DU at 4:29 AM on September 13, 2012 [4 favorites]

What if the universe inside each atom is actually this universe? What if there's only one electron, and one proton, and one neutron, and they are time-looped through the end/beginning of time? What if time itself does not actually exist, rather is just our perception of the direction of entropy? What if the human mind is like radio waves through time, and the brain a reception system for these waves, rather than a broadcaster of them? What would the world be like if it was impossible to ask hypothetical questions?
posted by aeschenkarnos at 4:32 AM on September 13, 2012 [3 favorites]

Yeah, I decided to go 95% non-human microorganism a while ago. The 5% of me that's left gets to just sit back and enjoy the ride, although I now spend a lot of time slithering through sewers and absorbing other life forms through what used to be my skin. Also, I'm spending a ton of money on yogurt.
posted by orme at 4:36 AM on September 13, 2012 [8 favorites]

I have rosacea and still cannot quite come to turns with the microscopic Troma film that is evidently taking place on my face every day. Hurp.
posted by middleclasstool at 4:58 AM on September 13, 2012 [2 favorites]

The Buddhists have had it right all along, we are One.
posted by tommasz at 5:12 AM on September 13, 2012

Or Many. Many being the same thing as One. At which point one begins to think the Buddhists are just hedging.
posted by Sing Or Swim at 5:19 AM on September 13, 2012 [5 favorites]

I'm telling you, man. Turtles.
posted by Egg Shen at 5:27 AM on September 13, 2012 [4 favorites]

We are legion.
posted by empatterson at 5:27 AM on September 13, 2012

If anyone needs me I'll be in the corner, rocking backwards and forwards and repeating the phrase 'Get them off me' for the next day or two.
posted by spectrevsrector at 5:37 AM on September 13, 2012 [4 favorites]

Bragg on BBC Radio 4 today interviewed three scientists including Steve Jones on the cell. it would be an awesome podcast to listen to (can't link while at work)

apparently human genetic material makes up the amount of a half-leg with the rest of the body representing the amount of baterial genertic material. We were more human at the point of birth than we are now, what a factoid!

Also something to do with a form of malaria cell (i think my SatNav voice spoke over this section) having a type of chloroplast it it meaning that they are looking at the properties of weedkiller to help! I can't wait to get home and listen to it again, utterly utterly fascinating what pops up in biology researc
posted by Wilder at 5:44 AM on September 13, 2012 [2 favorites]

Oh - before the catatonia kicks in, the wonderful Radio 4 show In Our Time was on the cell today, if you need more of a mitochondrial fix.
posted by spectrevsrector at 5:45 AM on September 13, 2012 [1 favorite]

The first link's interactive showed every bug that is harmful to humans in some way except the eyelash, gross mofo.

*scrubs face until it bleeds*
posted by stormpooper at 6:16 AM on September 13, 2012 [1 favorite]

My shrink told me I'm not allowed to look at this kind of post any more.
posted by looli at 6:44 AM on September 13, 2012 [2 favorites]

aeschenkarnos: " What if there's only one electron, and one proton, and one neutron, and they are time-looped through the end/beginning of time?"

Dr. Feynman, is that you?
posted by symbioid at 6:46 AM on September 13, 2012 [2 favorites]

(or are you Dr. Wheeler?)
posted by symbioid at 6:47 AM on September 13, 2012

spectrevsrector: "If anyone needs me I'll be in the corner, rocking backwards and forwards and repeating the phrase 'Get them off me' for the next day or two."

So you're the lawn everyone's been talking about.
posted by symbioid at 6:48 AM on September 13, 2012 [5 favorites]

I'm afraid to read the links because I might want to eat sometime to day, but the feeling I get from the summary is that the James Nicoll quote about English taking other languages into the alley and beating them up for words also now applies to human biology.

All the people freaking out about the idea of being a monkey's uncle are going to love this.
posted by immlass at 6:51 AM on September 13, 2012 [1 favorite]


That assertion makes me sad, and is shortsighted (i.e. we die without bacteria.) There has to be some philosophy (Descartes?) behind the notion that we are ONLY human beings and any other living creature on us is a parasite to be feared.

I don't know, maybe I'm just sensitive to hand sanitizer. Or maybe I'm grasping for others to embrace the complexity of our environment.

(This could also be a clumsy self-defense of having a dirty stove.)
posted by Turkey Glue at 6:53 AM on September 13, 2012 [5 favorites]

Then I go look at exiled's home page and their top stories are all links to other sites like this one to yahoo news: crows hold grudges.

(That was once a great web site.)
posted by bukvich at 7:01 AM on September 13, 2012

Oh crap I meant to post that in the other thread.
posted by bukvich at 7:02 AM on September 13, 2012

If anyone needs me I'll be in the corner, rocking backwards and forwards and repeating the phrase 'Get them off me' for the next day or two.

Dude, they are you. If you got 'em all off, you'd be dead.

The implications of all of this is so fascinating, especially in terms of medicine. How much more could we understand about disease and normal body function if we understood what all the lifeforms that live in us/on us do? Our model of "human bodies as discrete entities fighting off invaders" is so simplistic in comparison. The only thing that makes me sad is that they are really at the very very beginning of this and so I'll probably be dead before the really cool stuff gets discovered and implemented.
posted by emjaybee at 7:05 AM on September 13, 2012 [3 favorites]

We're also tapestries ourselves: We are the universe for trillions of smaller organisms. Each of the Earth's 7 billion-plus human bodies contains about ten times more microorganism cells than human cells.

For a while, the Discovery Channel had this show called "Curiosity" where they had a different person delve into some random oddball question for an hour (I think the one where Adam Savage hosted was analyzing advances in longevity, and the episode was this sort of alternative future biography for him where he ended up with all sorts of body enhancements and then 1000 years in the future was this human/computer data cyborg who could download himself into different spare bodies when he wanted to). Anyway, they had one with Mike Rowe called "World's Dirtiest Man," which actually was all about this very issue (the microparasites and microorganisms which live on us, and why in some cases this may not be a bad thing).

Towards the end there was a scene that blew my mind - Mike revealed that at some point, as part of the project, a team of scientists had made a sort of Mike-Rowe-shaped model entirely of petri-dish growing medium, and then had taken sample swabs from each and every inch of skin and nook and cranny of his body (although, I think for dignity's sake they may have avoided the genitalia and rectum) and then applied the swabs to the model. Then they left it for a week in a sterile room to let everything grow. The final scene of this was the team showing Mike what the model looked like after that week - and the thing was COVERED with all sorts of different colonies of things. Ordinarily, our own immune systems and our hygiene habits keep them in check, but without that....
posted by EmpressCallipygos at 7:13 AM on September 13, 2012

So Bill Hicks was right when he said human beings are just "virus[es] with shoes?"
posted by entropicamericana at 7:35 AM on September 13, 2012 [1 favorite]

If anyone needs me I'll be in the corner

That's where the greatest concentrations of Tindalos Mites are.
posted by Drastic at 7:41 AM on September 13, 2012 [4 favorites]

So, the recent 'Alien' prequel isn't all that far-fetched, after all.
posted by armoir from antproof case at 7:45 AM on September 13, 2012

This stuff should not be surprising to anybody who has ever sat down and thought seriously about trying to nail down the idea of "species" with anything approaching rigor.

Life is random and wild, and it does what it does, and most of what it does is not affected at all by what we think of it or by the categories we use to help us do that.

I mean it's nice to have categories, and they do let you take some pretty spectacular reasoning shortcuts that get somewhere useful most of the time, but it doesn't pay to take them too seriously.

We do it, though. Constantly. To the point where our young worry themselves, some of them literally to death, that they just don't fit properly into whatever category they've been told or even decided for themselves that they ought to be an example of.

To me, the whole idea of identity as - as a man, as a feminist, as a parent, as a middle class middle aged white male, as a human being - seems broken and wrong. The correct response to "who/what am I?", it seems to me, is not some category name but the following:

1. I am this (waves hands in vague direction of own body)
2. Describe this.

So if "teeming multitude of tightly integrated organisms" is an accurate and useful partial description - and it probably is - why should that put me off my breakfast? After all, I'm not just eating for one but for leventy squillion.
posted by flabdablet at 8:04 AM on September 13, 2012 [6 favorites]

Our model of "human bodies as discrete entities fighting off invaders" is so simplistic in comparison.

It's worse than that since, in the trenches, they don't model the human body as a discrete entity fighting off invaders, but, rather, reductionistically look at individual systems in the human body without thinking real hard about what they might be attached to.

Hell, sometimes they can't even look at a whole molecule as a discrete entity. The big pharmaceutical company I used to work for was looking at making synthetic antibodies that would grab on to two different things while, after roughly a zillion years of evolution, mother nature makes antibodies with 2, 4 or 10 identical binding sites. What this means is that natural antibodies have avidity, the chance that, if one binding site lets go, another binding site might grab the target. I asked about this once (what can I say, I have a binding kinetics fetish) and was basically told, "Binding more things is more better. Amiright?"
posted by Kid Charlemagne at 8:10 AM on September 13, 2012 [3 favorites]

topofleftfoot via nervesinskinofleftfoot to painmonitorinbrain cc whitebloodcellappel

Alliance with Betadine weak. Dettol reinforcement counterproductive due to friendly fire. Ichor support ongoing. Opened negotiations with locals, no results yet. Advise.
posted by likeso at 8:15 AM on September 13, 2012 [2 favorites]

I love the idea that I am an ecosystem. I mean, I always knew that each person is basically a walking, talking ecosystem for much smaller organisms, but the articles in the FPP really bring the idea home in a totally awesome way.
posted by asnider at 8:19 AM on September 13, 2012 [4 favorites]

I am a coral reef.


The anemones tickle.
posted by Sys Rq at 8:20 AM on September 13, 2012

Me, I'm a jellyfish. A school of jellyfish. A flotillion of schools of-

Coffee. We want coffee.
posted by likeso at 8:24 AM on September 13, 2012

I loved the quote about our microbiome from the last article: "Birren likens it to a potluck dinner, where everyone brings something different to the table so everyone gets to eat."

Now I'm hungry! Here it comes all you little guys!
posted by TreeRooster at 8:31 AM on September 13, 2012

All that 'we are a simulation' crap is just deus ex machina creationism by other means, and is essentially religiously motivated.

There is absolutely nothing to be gained, and much to lose, through seeking to explain the world by invoking an invisible, impalpable, undetectable overarching agency, because it would have to be much more complex than we are-- since it would have all our complexity plus-- and it's amazing (and depressing) that it gets any traction whatsoever.
posted by jamjam at 8:48 AM on September 13, 2012 [2 favorites]

I'm all itchy now.
posted by kamikazegopher at 9:20 AM on September 13, 2012

Sleeper: The relationships between different organisms sharing a body is either symbiotic, commensal, parasitic, or pathogenic.
To be more precise, two different organisms can simultaneously have more than one of those relationships between them at a single time.

There is a tree disease (A) that kills its hosts, but wards off other diseases (B), and tends to kill hosts so slowly that the trees can reproduce. B is a quicker-acting killer. While acquiring disease A is not preferable to avoiding all threats, in instances where A, B, & C are present, having the symbiotic/pathogenic disease A is preferable (from the point-of-view of the tree's potential descendents) to not having this lethal disease.

There are human diseases of a similar nature - cow pox springs to mind. It definitely sickens the host, but prevents infections by the much more dangerous chicken pox.
posted by IAmBroom at 9:27 AM on September 13, 2012 [2 favorites]

This is (one reason) why Jurassic Park is fiction. If we attempt to clone ancient life forms from a single cell's DNA we will end up with a creature unable to survive - unable to digest, unable to maintain it's skin, unable to do all the things that all creatures require specific bacteria for. Somehow we would need to clone all the necessary bacteria and get them to the right locations at the same time.
posted by johngumbo at 9:31 AM on September 13, 2012 [4 favorites]

johngumbo, that presumes that the modern gut microbes are different and incompatible.

To a first-order approximation (close enough for the T. Rex to reach sexual maturity), alligator feces transplants might work.

Which reminds me - has anyone seen my lizard poo frontloader?
posted by IAmBroom at 9:48 AM on September 13, 2012

This post is amazing.
posted by molecicco at 4:05 AM on September 13


I should have mentioned in the FPP that if you skip the first link, none of it is likely to gross you out.

Also to avoid grossing people out I neglected to mention that the microorganisms we host add up to close to a kilogram of our weight
posted by Sleeper at 9:48 AM on September 13, 2012 [2 favorites]

One of the reasons I have no patience for people that are prissy about "germs!" and carry hand sanitizer everywhere. The other is that they are irritating.
posted by bongo_x at 10:21 AM on September 13, 2012 [2 favorites]

So if "teeming multitude of tightly integrated organisms" is an accurate and useful partial description - and it probably is - why should that put me off my breakfast? After all, I'm not just eating for one but for leventy squillion.

That's not you, it's your gut bacteria talking.
posted by sebastienbailard at 11:09 AM on September 13, 2012 [1 favorite]

I asked for information about this subject on another web site and was led to the following chart.

It shows that endosymbiosis has happened multiple times throughout the history of life, just as the viral insertion of DNA into a species's genome has happened countless times.

I was looking for more information on that and I found the research paper of which that chart was an illustration:
The plastids of Chlorophyta and plants, Rhodo- phyta, and Glaucocystophyta are... derived directly from a cyanobacterium. These three lineages may or may not be descended from a single endosymbiotic event. All other lineages of plastids have acquired their plastids by secondary (or tertiary) endosymbiosis, in which a eukaryote already equipped with plastids is preyed upon by a second eukaryote. Considerable gene transfer has occurred among genomes and, at times, between organisms.
I've been wanting to find out about how, as in the FPP, research areas like the ENCODE project and studies of endosymbiosis could cross-pollinate. When I found the above link, I found this sitting right next to it on The Google:
Eukaryotes – cells with nuclei – have inhabited Earth for ~1.2–1.8 billion year (Knoll et al. 2006), are major players in biogeochemical cycling, and include lineages that are the causative agents of numerous global disease (e.g., malaria, African sleeping sickness, amoebic dysentery). The most familiar eukaryotes – plants, animals and fungi – dominate the visible landscapes of terrestrial systems. Yet, these three lineages represent only a small fraction of the estimated 35–55 eukaryotic lineages that may be of comparable age.

....Here we focus on the recent transformation of hypotheses on the origin and diversification of eukaryotes that have occurred with the rise in molecular data (i.e. multigene sequencing, genomics). This increase in molecular data is the result of a confluence of factors including development of the polymerase chain reaction (PCR) and subsequently improvements in high-throughput sequencing of expressed sequences (ESTs) and whole genomes. We first focus on the origin of eukaryotic features, highlighting the compelling evidence for the chimeric nature of eukaryotic genomes.
Eukaryotic genomes... That is to say, the genomes of us and almost every non-microorganism you can think of is a chimera. which is sort of funny because our last president called in a 2005 State of the Union address for the banning of chimeras

The kidnapping of bacterial cells followed by their transformation into mitochondria or chloroplasts has happened multiple times in the history of life. Evolution keeps coming up with different variations on the same nearly-ideal solution--for example, eyes in animals have evolved more than forty different times. Richard Dawkins describes this in the chapter "The Forty-Fold Path To Enlightenment" in his book Climbing Mount Improbable. His central point in that book is to illustrate the amazing complexity that can come from the deceptively simple process of natural selection making small changes in a species over time, just as a mountain can be climbed with a series of small steps. The theory of endosymbiosis is fascinating to me because it seems to be a relatively large leap, a radical departure from the normal baby steps evolution takes.

Cross-transfer of genes is surprisingly common in biology. I recently read the Pulitzer-winning book The Beak Of The Finch and learned about cross-transfer of genes by crossbreeding:
"Hybridization... provides favorable conditions for major and rapid evolution to occur. ....[About 10%] of known bird species are known to have bred in nature with another species and produced hybrid offspring. ....It produces novel combinations of genes, as well as new alleles. ....Among plants the intercrossing of species can create new species and it can do so literally overnight. ....Somewhere between a third and a half of all the green things on this earth, and at least half of the world's flowering plants, arrived by the mixing of genes from separate species.

....Certainly it is rarer among animals than plants, but among birds and many other groups of animals, it seems, hybridization is widespread. It is common in toads of the large genus Bufo and in many families of insects. It is extensive among fish. ....[Darwin's finches speciated long ago into about a dozen different species, including a vampire bird, but] the finches are not yet carved completely apart from one another or from the ancestral stock, from the line of birds that first colonized the islands millions of years ago. If the chisel were not flying fast, the work of the carver would soon disappear without a trace, fusing back into the block of the living stone.

This same tension between fission and fusion runs through all the kingdoms of animals and plants. Everywhere hybrid swarms are rare; good, solid, more-or-less-separate species are common. Yet in many of the birds... fish... and in almost all of the green things growing around us the genes are intermingling. The chisel is hard at work daily and hourly in every landscape on the planet.

....If species were created once and for all, if they all came tumbling to life finished and polished, as Milton paints them in Paradise Lost, then each species of Darwin's finches would possess a fixed, permanent, never-changing set of genes. But genes are not fixed. The one hundred thousand genes of Darwin's finches are shuffled and cut in every generation, like a mammoth deck of cards.

....When stressed in a petri dish, many cells of E. Coli, whose normal habitat is the human gut, will even open pores in their membranes and take in DNA from outside their cell walls. Strands of naked DNA are always floating around these bacterial colonies like scraps of old newspaper. The living cells open up, take in the naked DNA, and patch some of it into their own genes. The process is known as transformation, and it can be stimulated by the stress of unfriendly chemicals or ultraviolet radiation.

....You don't find [extremely chaotic environments] under natural conditions, but you do find them in the havoc that human beings leave in their train. Our arrival, Anderson says, 'can provide strange new niches of hybrid recombinations.' Thus, our disturbances hybridize both the environment and the species. We are hybridizing the planet.

....Western hospitals started to use antibiotics regularly in the 1950s, and resistance appeared within a year or two. One out of every three patients in every Western hospital [in 1993 was] on antibiotics [possibly more now], and antibiotic resistance is increasing so rapidly that many physicians are calling it a global epidemic.

....So far, despite all our plagues, we have been lucky. In principle, a random mutation or hybridization event could someday create a virus that combines the airborne, infectious qualities of fly and the deadly, long-latency, slow-killing qualities of AIDS. It hasn't happened yet, but there is nothing in Darwin's process to prevent it, and the larger the pool of human beings on the planet, the more viruses are jumping in.

'Our only real competition for domination of the planet remains the viruses,' the microbiologist Joshua Lederberg once said. 'The survival of humanity,' he added, 'is not preordained.'
(I combined text from a bunch of different chapters, just picking out some of the most interesting tidbits. A lot of context was lost in the process; you'd have to read the book.)

Biology has been making my head explode lately.

posted by Sleeper at 11:54 AM on September 13, 2012 [4 favorites]

2. Mitochondria in human cells originated when the same type of bacteria that causes typhus disease raided one of our cellular ancestors and instead of hijacking it was pressed into service.

This is a really misleading way to describe Alphaproteobacteria
posted by Blasdelb at 11:56 AM on September 13, 2012 [1 favorite]

I combined text from a bunch of different chapters, just picking out some of the most interesting tidbits.

It is really difficult to get a strong grasp of a fast moving and somewhat complex collection of fields this way. I'd recommend this class to get started to anyone who is interested.
posted by Blasdelb at 12:05 PM on September 13, 2012 [2 favorites]

cow pox springs to mind. It definitely sickens the host, but prevents infections by the much more dangerous chicken pox smallpox.

There's still an ongoing mystery about where viruses even came from. All I really learned in biology classes is that every time you ask a question, the answer raises three more questions.
posted by tyro urge at 12:06 PM on September 13, 2012 [1 favorite]

The most disturbing, puzzling, awe-inspiring, and fascinating things I've heard that bacteria are doing with their hosts all concern Wolbachia, which infect incredible numbers of arthropods (insects, spiders, mites, etc.) and some nematodes:
It is one of the world's most common parasitic microbes and is possibly the most common reproductive parasite in the biosphere. Its interactions with its hosts are often complex, and in some cases have evolved to symbiotic rather than parasitic. One study concluded more than 16% of neotropical insect species carry bacteria of this genus,[1] and as many as 25-70% of all insect species are estimated to be potential hosts.[2]
Interest waned after the discovery[citation needed] until 1971, when Janice Yen and A. Ralph Barr of the UCLA discovered Culex mosquito eggs were killed by a cytoplasmic incompatibility when the sperm of Wolbachia-infected males fertilized infection-free eggs.[4][5] In 1990, Richard Stouthamer of the University of California, Riverside discovered Wolbachia can make males dispensable in some species.[6] It is today of considerable interest due to its ubiquitous distribution and many different evolutionary interactions.

Wolbachia species are known to cause four different phenotypes:

* Male killing: males are killed during larval development, which increase the rate of born females.[7]
* Feminization: infected males develop as females or infertile pseudo-females.
* Parthenogenesis: reproduction of infected females without males. Some scientists have suggested that parthenogenesis may always be attributable to the effects of Wolbachia.[8] An example of a parthenogenic species is the Trichogramma wasp,[6] which has evolved to procreate without males with the help of Wolbachia. Males are rare in this tiny species of insect, possibly because many have been killed by that very same strain of Wolbachia.[9]
* Cytoplasmic incompatibility: the inability of Wolbachia-infected males to successfully reproduce with uninfected females or females infected with another Wolbachia strain.

Several species are so dependent on Wolbachia, they are unable to reproduce effectively without the bacteria in their bodies.[10]

A nearly complete copy of the Wolbachia genome sequence was found within the genome sequence of the fruit fly Drosophila ananassae and large segments were found in 7 other Drosophila species.[26]

In an application of DNA barcoding to the identification of species of Protocalliphora flies, it was found that several distinct morphospecies had identical cytochrome c oxidase I gene sequences, most likely through horizontal gene transfer by Wolbachia species as they jump across host species.[27] As a result, Wolbachia can cause misleading results in molecular cladistical analyses.[28]
Wolbachia also harbor a temperate bacteriophage called WO.[30] Comparative sequence analyses of bacteriophage WO offer some of the most compelling examples of large-scale horizontal gene transfer between Wolbachia coinfections in the same host.[31] It is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that are typically considered highly stable and prone to genomic degradation.
posted by jamjam at 1:58 PM on September 13, 2012 [4 favorites]

There's still an ongoing mystery about where viruses even came from. All I really learned in biology classes is that every time you ask a question, the answer raises three more questions.

If you'll pardon my language, that author seems to have his head jammed pretty solidly up his Eukaryotic ass. To really look at the origin of viruses it is pretty silly to not even mention the oldest viruses. It turns out that while the viruses of bacteria, archaea and eukaryotes have evolved away from each other so fast for so long that sequence similarities between the capsid proteins (reasonably conserved parts that make up the hard shell) of viruses from each of the three domains of life can't really be found, there are strong relationships between them for each of three different kinds of shapes of structures if you squint a bit. This seems to indicate that not only do bacteriophages, arhaeophages, and eukaryotic viruses share a common ancestor, but common ancestors that each infected LUCA - the Last Universal Common Ancestor of all life. How cool is that? Personally, my money is on viruses evolving from the same pre-cellular entity that cellular life evolved from.
"Are Viruses Alive?
To consider this question, we need to have a good understanding of what we mean by "life." Although specific definitions may vary, biologists generally agree that all living organisms exhibit several key properties: They can grow, reproduce, maintain an internal homeostasis, respond to stimuli, and carry out various metabolic processes. In addition, populations of living organisms evolve over time.

Do viruses conform to these criteria? Yes and no. We probably all realize that viruses reproduce in some way. We can become infected with a small number of virus particles — by inhaling particles expelled when another person coughs, for instance — and then become sick several days later as the viruses replicate within our bodies. Likewise we probably all realize that viruses evolve over time. We need to get a flu vaccine every year primarily because the influenza virus changes, or evolves, from one year to the next (Nelson & Holmes 2007).

Viruses do not, however, carry out metabolic processes. Most notably, viruses differ from living organisms in that they cannot generate ATP. Viruses also do not possess the necessary machinery for translation, as mentioned above. They do not possess ribosomes and cannot independently form proteins from molecules of messenger RNA. Because of these limitations, viruses can replicate only within a living host cell. Therefore, viruses are obligate intracellular parasites. According to a stringent definition of life, they are nonliving.
There is a somewhat subtle point of what a virus really is that the author totally misses, but I think it really clarifies this question a lot,

If you were going to count the number of frogs in a pond, and somehow had access to technology that would let you, would you include the millions of eggs released from each fertilized egg sack as frogs in your final number? Similarly, if you were going to count all of the viruses on earth1, would you count the inert dead viral particles or the virally pregnant cells? What I'm trying to get at is that, while historically we've thought of a viral particle that infects cells when researchers have thought of viruses, it might make a lot more sense to think of viruses as infected cells that produce viral particles. Indeed, once you shift your perspective enough viruses - and particularly the viruses of microbes - seem a lot more alive. In addition to reproducing and evolving, the viruses of bacteria and archaea often produce their own energy in the form of ATP through fundamentally different mechanisms than their host uses, all but the smallest demolish their host's metabolisms - replacing it with their own metabolisms, they actively maintain homeostasis - often in ways fundamentally different from the way the host does, while they do not encode their own ribosomes many do alter the host's ribosome into a fundamentally viral one incapable of translating host RNA and optimized for translating viral RNA, they respond to external stimuli in their own unique ways, and hell, they even get infected by their own viruses.

If this is the kind of thing that interests you the review that he takes that figure from (As well as the slap fight the review sparked) might be fascinating. The combatants are both amazingly kind, generous, dignified, and understanding men, but really these three papers are Patrick Forterre and Elio Schaechter doing the academic equivalent of going Jerry Springer on each other while arguing about the nature of what a virus is.

Redefining viruses: lessons from Mimivirus
Viruses are the most abundant living entities and probably had a major role in the evolution of life, but are still defined using negative criteria. Here, we propose to divide biological entities into two groups of organisms: ribosome-encoding organisms, which include eukaryotic, archaeal and bacterial organisms, and capsid-encoding organisms, which include viruses. Other replicons (for example, plasmids and viroids) can be termed 'orphan replicons'. Based on this suggested classification system, we propose a new definition for a virus — a capsid-encoding organism that is composed of proteins and nucleic acids, self-assembles in a nucleocapsid and uses a ribosome-encoding organism for the completion of its life cycle.

What makes a virus a virus?
In a recent review, Raoult and Forterre (Redefining viruses: lessons from mimivirus. Nature Rev. Microbiol. 6, 315–319 (2008)1) proposed a dichotomy of the biological world, dividing it into 'organisms', those entities that encode a functional translational machinery, and viruses, those entities that have capsid shells instead. The implied definition of viruses, although highly relevant, does not rely on the most fundamental aspect of what makes a virus a virus: it breaks up and loses its bodily integrity, with its progeny becoming reconstituted after replication from newly synthesized parts. We propose that the defining attribute of all viruses is their disintegration and reconstitution, from the tiny geminiviruses (15–20 nm diameter; 2.5 kb DNA genome) to the colossal Mimivirus (400 nm diameter; 800 kb DNA genome). Importantly, disintegration and reconstitution are totally independent of time, with reconstitution occurring minutes, days, years or centuries after disintegration.

What makes a virus a virus: reply from Raoult and Forterre
The correspondence on our Opinion article (Redefining viruses: lessons from mimivirus. Nature Rev. Microbiol. 6, 315–319 (2008)1) by Wolkowicz and Schaechter (What makes a virus a virus? Nature Rev. Microbiol. 16 July 2008 (doi:10.1038/nrmicro1858-c1)2) has allowed us to clarify some of the elements of our virus definition1. The authors rightly insist that the phenomenon of disappearance and reappearance of a virus (eclipse phase) is a major characteristic of viruses. They then go a step further, however, to suggest that it is the most fundamental aspect of a virus and propose to use this feature, instead of the capsid, to define viruses. Although the eclipse phase is informative in terms of virus description and could be added to our virus definition, we think that such a feature cannot be solely used to define viruses, because it is a phenotypic trait that cannot readily be assigned to a particular gene or set of genes (unlike the capsid) in the viral genome. Consequently, a definition of viruses that is based only on such properties would have a pre-Darwinian flavour (similar to the prokaryote or eukaryote classification system).

1There are about 1031 bacteriophage particles on the planet. To get an idea of the scale of that number, it is twice as big as the mass of the sun in pounds. Similarly, even though phage are only around 125 nm long [For scale], which is about a fifth as tall as the wavelength of visible light, if you were to stack them on on top of the other end to end you would get a spire that would be 100,000,000 light years tall - it would stretch out an order of magnitude past the next galactic cluster.
posted by Blasdelb at 2:39 PM on September 13, 2012 [16 favorites]

As within, so without.

This is a good start to understanding ourselves, the next point is to recognize that these multitude of organisms that live within us are part of a larger ecosystem that is constantly interacting and evolving.

I think we are less like planet earth with a discrete boundary, and more like a city or country with permeable borders and constant immigration, emigration and trade.
posted by psycho-alchemy at 9:35 PM on September 13, 2012

"2. Mitochondria in human cells originated when the same type of bacteria that causes typhus disease raided one of our cellular ancestors and instead of hijacking it was pressed into service."

This is a really misleading way to describe Alphaproteobacteria
posted by Blasdelb at 11:56 AM on September 13 [1 favorite −] Favorite added! [!]
You're right that it's not really the same bacteria, or exactly the same type. They're just related. I should have phrased that differently.
posted by Sleeper at 12:16 AM on September 14, 2012

Sleeper: "The relationships between different organisms sharing a body is either symbiotic, commensal, parasitic, or pathogenic."

Most properly, the term symbiosis is used as an umbrella term encompassing the whole spectrum of behaviors from commensalism to parasitoidism, and simply refers to two organisms living in each other’s presence in a metabolically intimate way. The spectrum can be seen as a tradeoff between two strategies, or of course a mix between the two. The symbiont can care little for its host and make as many infectious particles as possible at the host's expense, thus increasing virulence (how much the parasite fucks up its host as a consequence of infection). In this strategy it doesn't matter so much that the host becomes quickly unsuitable because the parasite has already found replacement hosts sneezed on, or transmitted to, by the time that happens. Or it can do the opposite and try its best to reduce impact on the host, shed infectious particles slowly or even not at all, and thus not need to spread to quickly because it will last a while in each host. Commensal symbionts are at that end of the spectrum, and have become so adept at not fucking up their host as to actually benefit them in some way. On the other end are parasitoids. These are the parasites that not only fuck up their host in their race to infect as many more hosts as possible, but spend the majority of their life cycle doing so and ultimately sterilizes, kills, or sometimes consumes the host in the process. The Xenomorphs from the movie Alien are a beautiful example of these sorts of parasitiod strategies, each inspired by real fucked up shit in nature.
IamBroom: "To be more precise, two different organisms can simultaneously have more than one of those relationships between them at a single time."
Oh man do I have the coolest paper to show you guys,

Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism
Bacteriophages are known to carry key virulence factors for pathogenic bacteria, but their roles in symbiotic bacteria are less well understood. The heritable symbiont Hamiltonella defensa protects the aphid Acyrthosiphon pisum from attack by the parasitoid Aphidius ervi by killing developing wasp larvae. In a controlled genetic background, we show that a toxin-encoding bacteriophage is required to produce the protective phenotype. Phage loss occurs repeatedly in laboratory-held H. defensa–infected aphid clonal lines, resulting in increased susceptibility to parasitism in each instance. Our results show that these mobile genetic elements can endow a bacterial symbiont with benefits that extend to the animal host. Thus, phages vector ecologically important traits, such as defense against parasitoids, within and among symbiont and animal host lineages.

One of the many problems farmers of various kinds of legumes need to deal with is the pea aphid. They reproduce stupidly fast and live by sucking the sap out of the plants, here is an awesome electron micrograph of one in action. However, while they are terrifying parasites of legumes, they have their own yet more horrific parasites, a parasitoid wasp. Here is a really nice close up picture of one doing its thing, here is video of the act, and here is a brain meltingly horrific video of a dissection of the aftermath 8 days later. Basically, they deposit their eggs in the a pea aphid and the larva feeds on it, developing there for about a week, and then consuming the host from the inside out like a Xenomorph. When it’s done, the wasp larva dries the aphid’s cuticle into a papery brittle shell and an adult wasp emerges from the aphid mummy. Farmers love these things, and can even order their mummies online these days, because they are so effective and, I imagine, so brutal to these critters destroying their livelihoods.

However, farmers noticed that the wasps didn't work as effectively on all of the aphids, and so researchers went to work figuring out why. It turns out that all aphids have a primary bacterial endosymbiont living inside their cells, in addition to and just like a mitochondria, and that many have some combination of five other secondary endosymbionts. Interestingly, two of those other five, Hamiltonella defensa and Serratia symbiotica have been shown to confer varying levels of resistance to the parasitoid wasp, allowing the aphid to survive infection. The relationship these endosymbionts have with the aphid, as well as the primary endosymbiont, is hard to classify as they confer a fitness cost in the absence of the wasp but a significant fitness boost when the wasps are around and trying to infect the aphids. However, it turns out that there is yet one more layer to this story,

At least for H. defensa, the reason why some strains are fully parasitic and provide no protection against the wasps while others are at least plausibly commensal and do provide protection, is a bacterial virus that infects the endosymbiont, even while it is inside the eukaryotic aphid cell. To understand why it will require a bit of knowledge of how some bacteriophages work, I'll get back to H. defensa I promise. You see, even though many figure obligate parasitism to be a central feature of what a virus is, particularly folks who work only with eukaryotic viruses, the truth is a lot more complicated. Most bacterial viruses, also known as bacteriophages, have a clear dividing line between two strategies. The simplest and most virulent phages will always immediately shut down their host’s metabolism upon infection and replace it with their own. Within a short period of time, generally between 20 and 80 minutes, the phage will have used the host cell to replicate its genome, build new protein particles, packed those particles with the genome and lysed the cell; setting loose 30-3000 new inert infectious particles made of only protein and nucleic acid. These are known as obligately lytic phages, and have profound implications for the treatment of bacterial infections (PDF). Most phages however, use a mix of this strategy and another one known as lysogeny. These temperate phages will, at the beginning, decide to either virulently infect, producing particles at the dramatic expense of the host, or hide in the host’s genome and inactivate all of its many host lethal genes. Generally it does this by expressing a transcriptional repressor that prevents expression of everything but the repressor, which incidentally protects the host from subsequent infection by related phages. However, some temperate phages will allow for expression of a cassette that will perform some function of benefit to their host, they might as well since they are completely dependent on their host's wellbeing while in this stage of their life cycle. These kinds of phages are at least difficult to blithely classify as obligate parasites, because for the majority of their life cycle they are in fact commensal.

It turns out that there is a temperate bacteriophage called APSE, which is common in H. defensa populations in the aphids, that encodes for a cassette of genes that causes H. defensa to attack the wasp larvae while it is hiding in the genome of its bacterial host. This makes for a really fascinatingly complex system of interdependencies for each of the agents involved. The phage, the bacterial symbiont, and the aphid are all each united in their interdependent need to combat the wasp that kills all three when it succeeds, but at the same time both the phage and the bacteria are dependent on the wasp to apply pressure on the aphid to keep them around. Additionally, the wasp the bacteria, and the phage are all completely dependent on the aphid’s sap sucking ability to sustain them, and the aphid is totally dependent on the farmer to continue growing legumes in massive vulnerable monocultures. Furthermore the farmer and the legumes are dependent on the wasp to combat the aphid and largely helpless against the bacteria and the phage. At the same time, despite all of the interlocking incentives toward cooperation, there are also incentives towards cheating. The farmer has an incentive to ‘cheat’ and neglect to buy aphids every so often, because they still benefit from the fitness cost caused by the aphid not rejecting the bacteria or the bacteria rejecting the phage. Similarly, the aphid has an incentive to cheat both the bacteria and the phage to cure itself of them and bet on the farmer not buying aphid mummies full of wasps that year. The bacteria also has an incentive to cheat the aphid by curing itself of the phage, and itself also bet on the farmer not buying mummies that year.

More information can also be found in the PI’s PNAS paper.
posted by Blasdelb at 7:32 AM on September 14, 2012 [4 favorites]

That paper should come with an Ennio Morricone soundtrack.
posted by flabdablet at 9:09 AM on September 14, 2012

I should probably get better at posting these things earlier in threads.
posted by Blasdelb at 11:12 AM on September 14, 2012 [1 favorite]

Blasdelb, you had me at "parasitic wasp".
posted by IAmBroom at 12:05 PM on September 14, 2012

Another fun body-sharing-partner for humans: The acanthamoeba.

Researchers Warn Contact Lens Wearers Of Parasite That Gnaws Through Eyeballs.

Carry contact lens solution with you while wearing contacts. Don't rinse them out in tapwater.
posted by Sleeper at 3:04 PM on September 26, 2012

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