Putting the life back in science fiction


And We Thought Hibernation Was Simple 2: now with bleach

Most of a year ago, I posted about the first tardigrade genome sequence, which apparently had a lot of bacterial genes in it.  Now, another group has published another genome (io9 article here, report here), and this apparently changes everything, possibly in a better way.  Or possibly, we’ll see some horror move remake of The Fly, only with Ramazzottius varieornatus at the hybridizing end (paging John Scalzi.  I’ve got your vacuum-sucking warriors right here). Continue reading

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The dust of ages

I came across this little bit when listening to NPR’s On The Media.  The episode is entitled “Digital Dark Age” which of course pricked my ears up immediately, as the digital dark age is something I dealt with in Hot Earth DreamsThe whole hour is worth listening to, but the weird idea I wanted to focus on is the idea of using artificially generated DNA for long-term data storage, an idea put forward by Dr. Nate Goldman in this segment.

Superficially, this is a great idea. Dr. Goldman is working on this idea as a way to store the huge amount of genomics data he has to curate at the European Bioinformatics Institute.  DNA is pretty stable and information dense, so if it’s possible to cheaply generate long DNA sequences and to cheaply read them, it’s a good form of ROM (Read Only Memory).  Dr. Goldman develops this into an idea of caching the great works of civilization in some sort of time capsule that starts by explaining what DNA is and how the code works, then progresses to simple decoding examples, and finally to the whole earth encyclopedia, or whatever is supposed to be in the data cache.  DNA is certainly more durable than known electronic digital media and is smaller than durable analog media like baked clay tablets, so superficially it has a lot going for it.

One little problem with this scenario is the idea that it’s easy to generate and read DNA.  It’s easy now, but I remember how hard it was even 20 years ago when I was in grad school.  This is a new technology.  Indeed, Dr. Goldman doesn’t think this technology will be financially viable for another decade or two, although it’s borderline technologically viable now.

Still, DNA ROM works better if we’re talking about a hypothetical sustainable civilization, as opposed to leaving some sort of time capsule for the next civilization 5,000 years from now or whenever.  DNA is not the kind of storage medium that will allow people to jump-start civilization from a hidden cache.  It’s just too tricky to read and write, even though DNA has demonstrably lasted tens of thousands of years in fossil bones under ideal conditions.

It’s even more suitable when we’re talking about interstellar colonization, where information needs to be stable for thousands of years.   Not only can the genomes of potentially useful organisms be stored as DNA, all the other information the starship needs to curate can be stored as DNA as well.

The other little problem with using DNA to store data is that having such technology widely available means that high-level synthetic biology will be available to anybody who wants it.  After all, if the equivalent of a laptop can generate as much DNA as your average genome, how many more bits of equipment are needed to twirl that DNA into chromosomes, insert it in a cell, and make a new eukaryotic life form?   Letting this kind of technology be available to the public is something that is currently forbidden, at least in current American society.   What kind of societal changes would required for people to believe that such technology is safe?

Still, it’s another possible technology for a hypothetical sustainable and starfaring civilization.  Perhaps in the future, we’ll have computers that are as much biotech as chips, where spam is something you feed your machine to support its self-repair function, rather than something you delete from your inbox.

Or maybe we should try to baked clay tablet thing…

 



And we thought hibernation was simple…
November 24, 2015, 7:52 pm
Filed under: colonizing space, Real Science Content | Tags: , ,

Unfortunately, the article is behind a paywall at the moment so you can only see the abstract, but PNAS just published a draft genome of the tardigrade Hypsibius dujardini.  Here’s the Yahoo news piece on the finding.

Basically, tardigrades are microscopic animals that are renowned for their ability to be frozen, boiled, desiccated, subjected to a vacuum on the outside of the space shuttle and so forth.  They’re the ultimate survivors among animals, and I’m pretty sure that every SF writer who thinks about putting astronauts in hibernation is thinking something along the lines of copying tardigrade’s toughness in humans through some futuristic technology.

But there’s an itty bitty catch.

If the draft genome is right (and there’s no reason to think it isn’t), tardigrades just took the record for having the most foreign DNA in their genome of any animal, about 16%, double the previous record holder.  They’ve got genes “derived from diverse bacteria as well as plants, fungi, and Archaea.”

My first thought was of Brin and Benford’s Heart of the Comet and the weirders (I still like that book), and then that ooh, massive horizontal gene transfer will take us to the stars!  Yay!  We get to go as gardens.

Then I read some more and found out that tardigrades’ toughness comes at a price: their DNA falls apart when they’re desiccated, and their cells get leaky as they rehydrate.  As a result, DNA from the surrounding environment gets taken up into their cells and, where it’s useful somehow, it gets taken into the tardigrade’s rebuilding genome.  Now bacteria do this all the time, so what’s unique here is that an animal has separately evolved the trick.  It’s one hell of a trick too, being able to repair eukaryotic DNA at that level and to usefully incorporate genes from wildly different organisms.  There’s a lot to be learned from these cute little water bears.

Still, this puts a whole different spin on putting people into hibernation to send them into deep space and to the stars.  It looks like tardigrades don’t have a magical way to avoid the damage caused by freezing.  Instead, it looks like they’re amazingly good at picking up the pieces afterwards and rebuilding themselves.  Presumably, that’s what we’ll have to learn to do (assuming it’s possible–tardigrades don’t have big brains),  if we want to turn people into corpsicles and back again without damage.  At the moment, the only methods we know of involve the use of either narrativium or handwavium, and both these elements are really unstable.

 



Three solutions to the Fermi Paradox
March 27, 2015, 4:23 pm
Filed under: science fiction, Speculation | Tags: , ,

Wow, didn’t realize I hadn’t posted in so long.  I got busy with life and writing.  Here’s something that I was originally going to put in the book, but it doesn’t really fit there.  It’s thoughts about how human experience might explain the Fermi Paradox.

Now, for one thing, I don’t think it’s much of a paradox.  After all, as XKCD explained in “Alien Astronomers”, it would be almost impossible for a radio telescope on Alpha Centauri to pick up our radio broadcasts.  Military and research radar beams, yes, but not our ordinary chatter.  One critical point is that broadcasting powerful radio signals takes a lot of energy, and that’s expensive.  If it’s more cost effective to be efficient, then we’ll do it (as we have with broadcasting and intercontinental cable) and that makes us more radio-invisible.  At our current level of technology, the galaxy could be brimming with civilizations, and we couldn’t see them, nor could they see us.  Being blind isn’t much of a paradox.

Of course, the question is, why aren’t the aliens here already?  If they’ve had even a million years’ more civilization, shouldn’t they have starships?  Well, here’s another answer: starships are expensive, because at high speeds, they’re a drag.  This came out of an arXiv paper (link), and the pop-sci version on Io9.  The basic point is that for a starship traveling at high speeds runs into photons from the Cosmic Microwave background, and if it’s traveling fast enough, those collisions generate about 2 million joules/second in energy, which seems to act like frictional energy slowing the ship down.  So not only does a starship have to hit those high speeds, it has to continuously generate more thrust as particle collisions slow it down.  You can’t just accelerate a starship and coast to another star, except at really low speeds which would take thousands of years to get between stars.  Do you know how to make a machine that continuously functions for thousands of years?  That’s a non-trivial challenge.  So there’s answer #2 for the Fermi Paradox: space isn’t slick enough to coast.  At high speeds, the CMB acts like an aether and causes friction, requiring continuous acceleration.

Answer #3 for the Fermi paradox is the one I was going to stick in my book, which is about what the Earth will look like if the worst predictions of climate change come to pass, and humans don’t go extinct.  This scenario could also explain the Fermi Paradox.  Basically, in the roughly 500 years of the Industrial Revolution (and yes, I know that it was much longer in the run-up), we’ll have burned through all our fossil fuels, our available radioactive elements, minable elements from aluminum to phosphorus, groundwater, and so forth.  After we use up all the cheap energy and readily available raw materials, we’ll be stuck recycling everything using solar and gravitational energy (or biofuels, PV, wind turbines, and hydropower, if you want mechanisms) for hundreds of thousands to millions of years, until the Earth can generate more fossil fuels. Perhaps we had a brief window in the 1970s when, if we’d gone for it and known what we were doing, we *might* have put a colony on the moon.  Highly unlikely, but possible, and the chances of that colony surviving would be fairly low.  We can’t get to Mars now (due to little problems like radiation in interplanetary space), and if we don’t get nuclear fusion to work real soon now (the 1970s would have been a good time for that breakthrough, too), we’re going to be downsizing civilization pretty radically in the coming century, rather than going to Mars or beyond.

Let’s assume that humans are relatively normal for sapient species, in the sense that we got our rapid spurt of technological advance by using up all the surplus energy that their planetary biosphere had squirreled away for the last 300 million years.  By the time we understood the true state of our world and the galaxy, we also realized we were in trouble, because we were already going into a time of overconsumption and too-rapid population growth. By the time we become technologically sophisticated enough to possibly colonize another planet, we won’t have the resources to do so.  Indeed, we’ll be forced to use any terraforming techniques we work out on the Earth just to keep it habitable.  Once we’ve survived this peak experience, we’ll be a mature civilization (or more likely civilizations), but we’ll also be radio-quiet, highly resource efficient, and totally incapable of interplanetary travel, let alone interstellar voyaging.

That’s the #3 answer to the Fermi Paradox: scientific development marches in tandem with resource extraction, and it’s impossible to become sophisticated enough to colonize another planet without exhausting the resources of the planet you’re on.  It’s possible that the universe is littered with ancient  sophisticated civilizations that have already gone through their peak resource crisis and are quietly going on with their lives, stuck on their planets, kind of like kids who went to college to change the world and got stuck with crushing college debts and jobs that weren’t their dreams.  In our case, we’ve still got a billion years or so left before Earth becomes totally uninhabitable, so it’s not horrible to be “stuck” here, on the one planet we’re evolved to live on. It’s just sad for those of us who thought that Star Trek looked like a really cool way to live.



Interstellar Civilization and Cthulhu

Time for something different. Admittedly, it’s inspired in part by Matt Wedel’s recent musings on how to make a proper Cthulhu idol. Since it’s July, I figured I’d trot out something I’ve been musing about. It has to do with vernal pools. And Cthulhu. And interstellar civilization.

Vernal pools, in case you don’t know, are rain-fed pools that crop up in the spring. I’m used to the California ones, which feature a wide variety of (typically rare to endangered) species that act as typical aquatic or wetland species, but only for the few weeks to months that the pools last. They have a couple of neat properties that are relevant here. One is that vernal pool species have a number of ways of dealing with the inevitable death of the pool, from flying to another pool to going into hibernation to producing propagules (seeds, eggs, etc) that can survive up to a century before they grow once a new pool forms. The other thing to know is that organisms in the pool typically start at the small end (fairy shrimp, algae), followed by bigger ones (tadpoles, small aquatic plants), followed by “large” predators (dragonfly larvae, beetle larvae), followed finally by the really big things (ducks, garter snakes) as the pool dries. It all happens quite fast, a miniature serengeti, as someone called it.

If you don’t know what Cthulhu is, well, what can I say? Go read The Call of Cthulhu, and come back later. But this is more about Lovecraft’s whole mythos of critters that lived in deep time and still live here and there, ready to jump out and go boo. Erm… Right.

Lovecraft didn’t know much about math or biology, for which I don’t blame him. It wasn’t his thing. Still, rather a lot of science has floated under the bridge since he wrote in the 1920s and 1930s, so I’d suggest it’s high time to retcon the Cthulhu mythos into modern science. That, and it’s July. In that spirit, I’d like to suggest an interstellar civilization composed of Mythos monsters, and based in part on the model of a vernal pool.

Let’s start with our galaxy. By most measures, there seem to be millions of potentially habitable planets out there, but equally, in our world, we don’t see any evidence of interstellar cultures. This is slightly bizarre, as sun-like stars have been around from something like 500 million years longer than our sun has existed. One would guess that, if interstellar civilization could exist, it would exist, and that furthermore, it would have colonized Earth long ago. That is exactly what Lovecraft posited, with his fossil cities in At the Mountains of Madness, The Shadow Out of Time, and elsewhere. Personally, I think his reasons for why we’re not over-run by alien beasties are a bit weak, so this is where the retcon starts.

The big problem with interstellar civilization is that traveling between stars is horribly energy and resource expensive. Lovecraft got it right, when he talked about species migrating between the stars, rather than commuting (although his Outer Gods seem to not have that trouble). It follows then that when a interstellar civilization colonizes a planet, resource extraction begins in earnest. We’re not talking about sustainability here, not by a long shot.

Since we know what a non-sustainable civilization looks like (we’re living in one), we also know that, absent major changes, such civilizations die out in a geologic instant. This may sound non-functional, but there’s a way out of it. If the interstellar civilization on a particular world can colonize one or more new planets before the civilization dies, it can keep going. Planets recover from civilization over a 10-65 million year period (thanks to geologic processes that allow the biosphere to recover, new oil reserves that gather surplus sunlight, and erosion that uncovers ore deposits), so it’s theoretically possible for a really clever interstellar civilization to persist indefinitely by constantly moving, leaving most of the hundreds of millions of habitable worlds in the galaxy fallow for most of the time. When the civilization ends on a planet, its constituents either leave, die off, hibernate, or leave some sort of remnant or propagule to grow when civilization comes again, tens of millions of years later. Granted, it’s tricky for anything to survive intact for tens of millions of years, but with god-like technology comes god-like hibernation abilities.

So what happens when civilization rains down on a planet? I suspect it’s a lot like what happens when a vernal pool fills. The little guys (elder things and their shoggoth bionanotech) show up first and most frequently. If the planet’s biosphere isn’t that suitable, that may be all that shows up, and they leave after they’ve sucked up the available resources to move on to the next suitable planet. If conditions are more favorable, the elder things are followed by all manner of beings: mi-go, the Great Race, and so forth, each preying on (excuse me, establishing trade relations with) the things that came before.

Then Cthulhu and his kind show up. They’re the megacorps, excuse me, the big predators. However, Cthulhu has an odd biology. According to the Call of Cthulhu“[w]hen the stars were right, They could plunge from world to world through the sky; but when the stars were wrong, They could not live.” In biological terminology, Cthulhu and his ilk use two strategies: interstellar travel (“plunging through the sky”), presumably if the stars are close enough for them to make the transit, and they also can go dormant (“could not live”), presumably through some amazingly advanced form of anhydrobiosis, to wait between boughts of civilization. Once Cthulhu’s kind is through ravaging a planet, the show’s over, and those survivors who didn’t flee settle in to wait for the planet to heal itself. This is much like what happens when a vernal pool dries to mud. The flowers bloom in the mud, and everything sets up to wait through another dry summer

Note that colonization isn’t an organized process, but then again, vernal pool community formation isn’t organized either. Every pool is different every year, and it depends on things like how fast the pools are evaporating and what animals are close enough to colonize the pools. Most of them can pass a year (or hundred) without needing water. Similarly, interstellar civilization is conditioned by how far a particular species can travel between stars and by what they need to survive on a planet, whether they can pioneer an uncivilized ecosystem (as the elder things can), or whether they need a civilization present to feed their great bulk (as with Cthulhu).

When Lovecraft talked about ancient cities, his biggest problem was lack of a viable dating technology. He wrongly assumed that species had been on Earth for hundreds of millions of year due to fragments throughout the geologic record, when in fact the planet was settled repeatedly, at different times, tens or hundreds of millions of years apart. It’s an easy mistake to make.

We can even understand the nature of Lovecraft’s Other Gods in this scheme. Azathoth, the blind idiot god (or demon sultan) at the center of the universe is pretty clearly the black hole at the center of our galaxy. Without it, this galaxy wouldn’t exist, so it is our creator in its own mindless way. Yog-Sothoth, the All-in-One and One-in-All of limitless being and self, is probably our galaxy’s equivalent of the Internet, possibly powered in part by the central black hole Azathoth. After all, if civilized species don’t know what’s going on on other worlds, how can they know where to migrate next? Nyarlathotep, “that frightful soul and messenger of infinity’s Other Gods, the crawling chaos,” is Yog-Sothoth’s equivalent of Siri, or perhaps Clippy the Paperclip, which may explain humanity’s generally negative interactions with it.

This leads to some interesting ideas. Paleontology in Lovecraft’s world is likely to be rather more interesting than our world’s paleontology. Think of what the remnants of an alien interstellar city would look like in the fossil record. Moreover, there would be a rather more sinister explanation for Earth’s mass extinctions, and the evidence would be rather different.

Of course, the ultimate question for humans is, when the stars come right and galactic civilization comes to this planet yet again, do we join in the madness and plunge between the stars with them, do we resist, or do we hide out until they go away, and hope we can survive on the scraps left behind?