The Shadow Biosphere

Hypothetical rendering of the Shadow Biosphere

The Shadow Biosphere:  Could life have appeared on earth more than once?  If so, where are they?

You’ve heard of the “Tree of Life”, right?  That we’re all descended from the same original spark of life on earth.  That every living thing on earth can trace their lineage back down the giant ancestral tree, leading eventually to that spot where life first appeared in a warm puddle on proto-Earth.  Why do we think this is true?  Because all life on earth is so astoundingly similar at the molecular level.  Much of the tiny building blocks and machinery in a living cell are common across all forms of life — DNA, RNA, proteins, the whole shebang.  When you compare a cell from a human to that of, say, a nematode, the inner workings of each organism’s cells are so similar that it sure smells like they’re working from the same blueprint – specifically, that they both evolved from a common origin.  So if you trace all of us back far enough, presumably that giant Tree of Life sprouted from just one seed.

In fact, someone smart calculated that the chances of all life *not* arising from a common ancestor are 10^2860 less likely, based on how overwhelmingly similar we all are at the cellular level.1  If we had it all to do over again, we living things would probably have found different solutions to various little biochemical problems — we might not use DNA, might not even use Carbon to become what we’re now famous across Starfleet for: being “Carbon-based life forms”.  Perhaps a lot of what we use in our cells is from historical accidents and happenstance, from evolution stumbling onto ever-more-efficient ways to do things.  The complex machinery we all share are just too complex to not share a common origin.

But who’s to say we haven’t done it all over again, back then?2    What if life appeared more than once, in independent times & places, throughout the Earth’s history?  The scientific evidence points to a single “biogenesis” blooming into the diverse range of life we know about on Earth today, but who’s to say there weren’t more biogenesis events?  Did our great-great-great…^1000 grandpa (a proto-microbe with a crude cell wall and some RNA) have a neighbor who moved away and never was heard from again?  We only know of life originating once (so N = 1) — so very hard to say anything with any decent scientific credibility.  Which is exactly where timeblimp comes in.

Meet your ancestor

We don’t really know much about how life formed on Earth.  It’s shocking how little we know.  In fact the general topic “origin of life” might be the single largest gaping hole in scientific knowledge today, aside from the hole in the ground where the superconducting supercollider was supposed to be.  But we can tell with pretty solid certainty that all of us (plants, animals, microbes, viruses, members of Dee-Lite) evolved from a single ancestor billions of years ago.  Let’s meet this hypothetical missing link for ALL species, a guy named LUCA — the Last Common Universal Ancestor.  From this crude little dude’s loins, all of us are descended.

We don’t have a sample or fossil of LUCA, of course — he’s purely hypothetical.  But based on how similar we all are to each other, we can figure out in pretty good detail what he looked like.  Specifically, he was a microbe.  So let’s call him an “it”.  She probably had the stuff that you find in any living organism’s cells today — some DNA, some RNA, the genetic machinery that made proteins using RNA.  It probably had the appliance that turns DNA into RNA, called the ribosome.  He almost certainly had some sort of cell membrane that kept his innards in.  And it probably used cellular division to reproduce.  So it’s pretty complex — that’s quite a long way down the evolutionary road.  Her descendants cooked up little variations here and there that eventually led to large enough differences to become completely different species, leading to the diverse life we have on earth today.

So here’s the question – if life were to start over again, would it necessarily produce some little organism that looks just like LUCA?  If life appears on another planet, say, would that planet have its own little microbe with DNA, RNA, and a ribosome?  Almost certainly not.  While DNA + proteins + all that other jazz are efficient ways to create a metabolizing reproducing organism, they by no means are the only way.  It’s more likely that most of what’s under LUCA’s hood were historical accidents from evolution’s trial and error over the first few hundreds of millions of years of life starting, probably strongly dependent on what raw materials were around to build with.  If life were to start over, it might wind up settling on completely different biochemical building blocks used in completely different ways.

Meet who your ancestor killed

We don’t have any evidence that a completely different branch of life ever got going, but the reasoning goes that since it started once (us), stands to reason it could have started again.  We ponder this often when we consider the possibility of life on other planets, but we don’t often consider it here on our own planet.  But after all, ours is the only planet we know for sure is *hospitable* to life.  So if life has ever started a second time anywhere in the universe, it probably happened here on Earth.

In fact it seems more likely that life did originate multiple independent times – how often does something this complex work right the first time?  It probably bloomed a few times, only to sputter to a halt when resources ran out, or was quickly snuffed out by a meteor.  Maybe proto-Earth had lots of warm nutritious tidepools all over, each with little sparks of life trying to get going.  What you’d then have are many little potential Trees of Life, each with their own particular ways of going about the day-to-day processes of living.  Maybe some of them stumbled onto using DNA, and others limp by using some completely different mechanism for passing on information to the kids.

Looking around at the Earth now, we see constant competition for resources, as various species battle it out for supremacy in the Terrordome we like to call natural selection.  Perhaps if there were multiple independent “Saplings of Life” that sprouted on earth, they also competed with each other for resources.  Maybe our friend LUCA had to slug it out with other life forms that used completely different molecular machinery to live.  Maybe it was stumbling across DNA that provided the key advantage for our ancestors, that gave them some advantage over other life forms that led them to be more successful in the harsh environment of Young Earth.  It could be that proto-life could cook up many different chemical ways to metabolize nutrients and pass along useful traits to offspring, but the DNA / RNA / protein toolkit turned out to be the fastest or most efficient.  So maybe it’s no surprise that we only see one form of life having survived to this day — our ancestor LUCA drove the others to extinction.

I’ve been talking so far 3  as if these independently-formed creatures flopped around billions of years ago, only to die out when outcompeted by our own ancestors.  But what if they didn’t die out?  What if these completely separate Trees of Life survived to the present day?  Maybe they didn’t go extinct, but have found a way to continue living on the Earth, perhaps all around us now.

This idea has been dubbed the “Shadow Biosphere”.  I’ve gotta say, in a world where the grandest overarching theory in physics is boringly called the “Standard Model”, a “Shadow Biosphere” is a refreshingly exciting name.  I first heard of this phrase from the endlessly entertaining Paul Davies, a famous physicist who is one of the rare breed of scientists who isn’t afraid to jump headlong into pure speculative (and possibly batshit insane) theory, especially if it’s a cool theory.  Much of what I’m writing here comes from his work.  But please stick around, I’m funnier than him.  The “Shadow Biosphere” is this hypothetical 2nd biosphere on planet Earth, evolved from a completely different biogenesis than our own, and up to now completely unnoticed by us.

They might be so different from us that they can exist in niches, exploiting things in the environment that we can’t.  In fact we might have pushed them to extreme niches, by out-competing them in our “normal” niches.  Perhaps they can survive at extreme temperatures, without water, or otherwise harsh environments where we haven’t looked yet.  Could there be strange life, lurking right now in some hard-to-reach corner of the biosphere?

Maybe they’re not crammed into some remote corner of the biosphere — maybe they’re all around us now, and we just haven’t noticed yet.  If they could coexist in our biosphere with us, it’s possible they’re all around us now, unbeknownst to us.  Cool idea, eh?  But before you picture some bizarre fantastical life form with three eyeballs and purple tusks hiding behind a tree, hoping not to be noticed, let me disappoint you by pointing out that any Shadow Biosphere in today’s world probably isn’t in the form of large, multicellular organisms, or we would have bumped into them by now.  We’re probably talking about microbes.  Unusual microbes.

They may look very similar to “standard” microbes — thanks to convergent evolution, they would probably evolve to look somewhat similar to microbes we know and love.  They might just all look like little blobs in a microscope — not obvious that they came from an independent biogenesis.  After all, we didn’t notice that the Archaea kingdom were so different from other microbes until we could do genetic analysis.  So it’s possible the Shadow Biosphere is fully interwoven with our own, and we just haven’t noticed it yet.

How do we find “life as we don’t know it”?

How the hell could we not notice this, you ask?  Let’s lay off the casual swearing, eh?  The tools we use to detect life generally assume life “as we know it” — unless its large and furry, we look for life using microscopic and genetic tools that have built-in assumptions, such as that all life contains DNA.  Some “life detection” techniques look for ribosomal RNA, and won’t detect you if you don’t have a ribosome.  (This piece of cellular machinery is something that anything alive appears to have, so looking for its DNA sequence amounts to a ‘universal’ detector for life.)  It could be really tough to detect these guys, since our biochemical tools (genetics, staining, etc) are “tuned” for life as we know it.  Weird life may simply show up as “negative” in every test we know how to do.  Developing a stain for, for example Ytterbium-based life, would be hard enough, but first you have to know that you should be looking for Ytterbium.

And “weird life” may be difficult to culture.  You might pick up some oddball microbe from a dirt clod outside your office that would net you a Nobel for sure, but you might not be able to keep it alive in the lab long enough to study it.  Maybe it doesn’t like agar, so it just shrivels up and dies on the little petri dish you made for it.  It’s likely you didn’t even know it was there — you didn’t even notice that it died.  With its little box of matchsticks.  It’s so cold, so so cold.  Don’t light those matches, little shadow-biosphere alien microbe!

Hell, this might even be true for “standard” life, 99% of which we can’t grow in the lab — much of what we know about microbes may be based on just the few percent that like to chomp on a layer of agar.  Maybe we should see what happens if we grow some dirt samples on a McRib.

What are we looking for?

So we’ve realized we’re hunting alien microbes that blend in perfectly with normal microbe society.  They may look like us, but they use a completely different set of biochemical building blocks for day-to-day living.  We’d have no idea what they might use, but we could wager a couple of guesses:

  • Molecule chirality — as it turns out, one of the weird facts about living organisms is that they only use “left handed” amino acids.  Many molecules can come in two different structural forms that are mirror images of each other, and as it turns out our bodies can only use one of the two types — right-handed amino acids can’t be metabolized by our bodies, even though they’re the exact same chemical formula.  Pretty much all life on earth has sworn off right-handed amino acids, at least life as we know it.  Since nearly all life made this choice, the choice must have been made pretty early on — perhaps right at the beginning during biogenesis.  Coming across a form of life that uses the other “chirality” of an organic molecule would be a potential clue they’re of separate origin than us.
  • UV light — ultraviolet light has a ton of energy, especially compared to the visible light that plants rely on for photosynthesis.  Too bad for plants (and us) that UV light is too energetic to harvest well — it tends to break down our molecules before it can be absorbed and converted to stored energy.  But if some other form of life stumbled across a robust enough molecular mechanism to capture it, it could rake in the energy while we stand around being sunburned by it.
  •  Different, unusual elements — remember “CHNOPS”?  No, that’s not from Blues Brothers (you’re thinking of SCMODS) — CHNOPS is a mnemonic for remembering the six most common elements found in life as we know it.  You learned this in 7th grade and haven’t used it since.  An alternative form of life might have wound up using a different set of elements, which would be a dead giveaway.  A famous example is the element arsenic, which has similar chemical properties as phosphorus and could potentially replace it if a bug finds itself in a phosphorus-poor, arsenic-rich environment.  Like Mono Lake in California, a stunning and desolate super-salty lake whose primary ecosystem includes millions of flies and billions of brine shrimp.  There’s a particular bug called GFAJ-1 living in Mono lake that might be the first known bug to use arsenic in its biochemical pathway.  We don’t think its part of any shadow biosphere, but cool nonetheless, and suggests that life could potentially get by without the standard CHNOPS suite of elements.
  • Alternative amino acids — if you remembered “CHNOPS” from junior high, you might also remember the fact that “life as we know it” uses 22 amino acids.  But there are many more possible amino acids that life just shrugs its collective shoulders at.  The Murchison meteorite, a gigantic rock that fell near a town in Australia in 1969, was analyzed and found to have perhaps 70 different amino acids in it.

Any candidates so far?   Nanobes

Back in 1999, Phillipa Uwins and colleagues found some extremely strange little organisms growing in some rock they dug up from a mine miles below the seafloor.  The microbes they found in a sandstone sample looked like pretty standard microscopic fungi, except for being really really REALLY small.  These “nanobes”, as they were called, looked like little tubes about 100 nm long and 20 nm in diameter.  Which is pretty damn small.  As it turns out, smaller than physically possible for a single cell to sustain itself.  To this day, we’re not sure if these things are alive or not.  If so, they could be a candidate for organisms from a Shadow Biosphere, according to Davies.

"You got a problem, punk? I thought so. Put me back in that rock."

These dudes are about a tenth of the size of the smallest known bacteria, and so we think they’re too small to fit all the machinery that they’d need to sustain life.  Hell, a single ribosome itself is about 20 nm across.  Stuff even just a couple ribosomes in there, and it ought to look like a snake after eating a couple deer.  Add in all the other stuff usually required by a metabolizing, self-replicating cell, and you’re way over the storage space available in these little dudes.  And yet they seem to contain DNA (or at least stain positive for the presence of DNA, according to Uwins).

Could they really be that small, and still be alive?  Sure, if they found completely different mechanisms for survival.  Take ribosomes, for example.  They serve to help convert RNA in the cell to proteins (translation), a step all living cells on earth perform.  Davies points out that about 70% of the cell volume is devoted to replication, so if an organism could somehow figure out a way to cope without it, it could theoretically get by with far less cell volume.  It would have to live a protein-free existence, but perhaps that could happen if you were an organism descended from a branch of life that never stumbled across proteins as a useful biomolecule.  Intriguing, eh?

Yes, but probably too good to be true.  It’s been over a decade now, and there’s nary a sign of follow-up research on nanobes.  The original researchers haven’t published since, and no one else has reported analyzing (or indeed finding) any other samples.  When a groundbreaking research area goes this eerily quiet, that’s usually a sign that something’s amiss.

I gather the general feeling is that their original samples may have been contaminated, perhaps by fragments from larger organisms.  (Does anyone remember losing antennae a few miles below the Australian coastline?)  But the original publication reports that the samples continued to grow in their lab after being extracted from the rock, even forming colonies large enough to be seen by the naked eye.  Hell, they found the stuff growing in the shape of a fingerprint on a petri dish, presumably after a lab researcher touched them (and likely are now also growing on that guy’s shower curtain, kitchen counter, etc.  I hope he washed his hands leaving that lab before draining the pope, if you catch my drift.)  Either they made this all up, or they did find something extremely tiny and extremely randy, to produce colonies all over their lab.

Any other candidates?  Check the basement.  Or Mars.

It’s interesting they dredged up this unusual life (if it ever existed) from deep underground.  In recent years we’ve also found a slew of “standard life” microbes living deep underground.  The surprising thing here is that the earth’s crust is a viable biosphere — vast colonies of microbes live down there, completely cut off from the surface biosphere, living off energy extracted from radioactive decay of rocks.  We’ve just recently discovered some of our own “standard life” living down there, so what else could be down there?

What makes this interesting from a shadow biosphere point of view is that deep underground could be a good place for proto-microbes just evolving on young Earth to get shelter from the meteorite bombardments that everyone in our solar system went through.  Earth used to undergo periodic bombardments by rocks from space, which likely turned the surface into an unimaginable hell.  If life happened to evolve in a quiet time then got obliterated during one of these periodic bombardments, we’d never know.  Except maybe it did survive — if it burrowed deep underground, maybe it could wait out the meteor storm and re-emerge during another quiet period.  Or, stay down there permanently, occupying to this day the deep-underground niche while we control the surface.

Or, early life could have clung to a rock ejected into space, where it remained in orbit to perhaps land back on Earth later (maybe millions of years later), “reseeding” earth with the primitive life.  Or Mars.  We’ve recently discovered that some Martian rocks make their way to Earth, and vice versa, especially when meteorites are kicking up dust and debris on both planets.  Some of the earlier iterations of life might have made their way to Mars, or come from Mars for that matter.  You all remember the big stink in the news around 1998 when it was claimed that fossils of what appeared to be nanobacteria were found in the Mars rock ALH84001.  Uwins pointed out in her nanobe paper how similar they appeared to be to the Martian rocks.  Unfortunately the Mars nanobes have met the same fate as her nanobes, with scientific consensus being they weren’t really alive.

Any candidates so far?  Clays

“Fine, nanobes are weird”, I hear you say, “but they aren’t as weird as I was expecting for a candidate representative from the Shadow Biosphere.  After all, they’ve got DNA, right?”  True dat.  Thanks for calming down, but how exactly did you get into my living room?  Nanobes, if they exist, would certainly qualify as weird, but at this point calling them members of the Shadow Biosphere (or even calling them living organisms) is pure speculation.  Are there any other candidates that don’t use the typical building blocks of life as we know it?  Have a seat on my couch, and let me tell you about clay crystals.

A formative moment in clay crystal evolution

Here’s the idea — clay, apparently, likes to form into little crystal structures in water.  The crystals grow over time, accreting more bits of silicate if they’re not jostled too much (such as at the bottom of a stagnant lake).  As layers of the crystal builds up, little imperfections in the crystal tend to get repeated — newer layers repeat the “mistakes” of preceding generations.  If a piece of crystal breaks off and tumbles away in the stream, it brings with it the particular pattern of mistakes or “mutations” it inherited from its “parent” crystal.  Cairns-Smith suggested the particular sites of defects in the crystal could be considered a way to store information (akin to holes in a punch card), and that information can be passed down among the crystal layer generations.  I know, I know — it’s kind of a stretch.  In fact the phrase “kind of” doesn’t apply here – this is a humongous stretch.  But let’s say a particular type of clay crystal pattern is more efficient, for whatever reason, at silting up a lakebed faster than other patterns.  By the natural course of events, that particular pattern will wind up silting up more of the local water supply — you might find it taking over the local lakes and ponds, forcing out other clay silting patterns.  In a crude form, then, this clay pattern is undergoing natural selection — random changes in its structure endowed it with some advantage, after which it outcompetes competing patterns.

This would mean that crystal formation in clay is an *inorganic* system undergoing a crude version of natural selection, in other words *evolution*.  It would exist in a gray area between the non-living and the living that up to this point we’ve never observed.  Bonkers, eh?  Well, sure — but that’s why we’re talking about it here, on  What makes this idea even cooler is that, if true, it’s surely *going on right now, all around us*.  Graham-Cairns actually proposed it as a possible link between non-living and living *organic* matter billions of years ago (as the self-replicating crystals might have given organic molecules a good place to stick to and work out their replication thang), but there’s nothing to stop these clay crystals to keep on evolving right to this very day.  Right now, crude completely inorganic life forms could be emerging out of the sandy silt at the bottom of your backyard pond — in fact the crude life *is* the sandy silt.  And it’s completely inorganic, a completely different ballpark from the biochemistry we use.  They wouldn’t use biochemistry at all, as we know it.


Finally, let’s end this pure speculation by heading down the hall to the academic department that has my favorite name of any science subdiscipline, by a landslide:  Astrobiology!  Isn’t that a cool name?  I want THAT on my business card.  Paul Davies has that on his business card – he’s a leading researcher in this very new area that focuses on looking for signs of life out beyond our little planet.  The astrobiologists (like Dr. Davies) are interested in the idea of a Shadow Biosphere because it might shed light on the likelihood life could originate elsewhere in the universe.  Since we’ve got exactly one case of biogenesis to study, we have no idea how common or unlikely life is – is it extremely difficult to get a successful “life” venture off the ground, or does it sprout up immediately all over the place?  We have no idea, since we’ve only got the one example to extrapolate from.

While “extraterrestrial life” is an unmistakably cool topic, it would normally be a bit too mainstream for us to consider here at  But I just couldn’t pass up this bit of interesting science from the realm of extraterrestrial origins of life.  In 200x, Jason Dworkin did an experiment where he mixed water, methanol, ammonia, carbon monoxide, and subjected the brew to UV light – just the kind of environment you’d find in a comet.  What happened?  Complex organic molecules formed!  And, when melted in water, the complex molecules formed little self-contained vesicles, wrapped in some sort of lipid membrane, with the complex organic molecules trapped inside.  Holy shit!  Pardon my French, but that’s pretty damn close to biogenesis.

If it’s really that easy for life to form, comets might have been delivering the building blocks of cells (organic compounds and lipid-like protective vesicles) to earth this whole time.  It could be that we owe the origin of life on earth to cometary delivery of the necessary building blocks.  It also just so happens that these little vesicles seem to absorb UV light, and fluoresce in the visible range.  This is just what you’d expect them to do, if they could use UV light for energy – a form of life that could soak in UV (as plants soak in visible-wavelength light) for a living would be expected to fluoresce a bit.  And if you weren’t protected by a UV-absorbing layer of ozone, you might find the necessary motivation to give UV light absorption a try.  Comets certainly don’t have ozone layers, and earth didn’t have one either until plants evolved to spit out oxygen into the atmosphere.  (Oxygen, of course, is the poop of photosynthesizing organisms.  Yes, you’re breathing plant poop.)

In Summary…

… much like many articles on this site, this particular idea is right on the line between science and wild-ass speculation.  Thankfully, there are a handful of tenured professors out there publishing on this stuff, so that’s close enough to reality to deserve consideration in an article here at  Many ideas once seemed preposterous at the time they were suggested to the scientific community — that the universe expands, that the earth’s surface is constantly undergoing plate tectonics, the idea of non-awkward small talk at a party — but these ideas eventually came to be accepted by most scientists.  The Shadow Biosphere could be the next idea to make the leap.  That is, if the Shadow Biosphere wants us to discover it — after what we’ve done to our regular biosphere, I wouldn’t blame them if they wanted to remain in the shadows.  Hell, if I were them, I might be actively trying to stop ongoing scientific research on this very topic, to silence any potential leak of news that I existed.  Come to think of it, has anyone checked on the nanobe researchers lately?

Some Footnotes

1.    Theobald, “A formal test of the theory of universal common ancestry”  (Nature 2010)

2.   This is the best sentence I’ve ever written.  Go back and reread it, imagining what it would look like completely out of context.  Here, here it is again:

But who’s to say we haven’t done it all over again, back then?

Epic.  If you’re not fighting back tears right now, as you sculpt the statue in my honor, then you my friend have a heart of coal.

3.   Yes, I talk while typing.  Well, not so much talk, as move my lips as I type.

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