Dennis Jackson ran a rare and used bookstore in San Francisco. I’m grateful for the happenstance that brought us together, though I’m afraid if you were able to ask him now, the feeling would probably not be mutual. I somehow got on his mailing list right around the time I was in town visiting an old friend. I love independent book stores, and the name caught my eye, “Chaosmos, carefully curated books, books from the obscure to the luminous.” Plus, there was a two-for-one coupon.

The bookstore smelled like books, not like peppermint mochas. I loved that. I was greeted by two bookstore cats, one right next to the door, the other lurking nearby. The bold one was a gray tabby who meowed emphatically. Being a keen observer of bookstore cats, I realized I must have come in around dinner time. The shy one was a redhead, lured out of the stacks by the promise of kibble. A middle aged black man proceeded to feed them. Soon he spoke to them in what sounded like a Scottish accent, “Come now, Leopold, you have your own. Let Molly be.”

Leopold and Molly. That is so cute. I took this opportunity to show off my erudition, “Leopold! Leopold Bloom? Does he eat with relish the inner organs of beast and fowl?”

The man turned and beamed warmly (he knows I’ve read Ulysses, and probably suspects I am fond of cats), “Indeed he does, though he generally settles for Friskies.”

I perused the aisles. As promised, there was a carefully curated collection of obscure and luminous books. Literature, poetry, mythology, history, metaphysics, art, philosophy and science. Many foreign language books, books on language, cryptography, artificial intelligence, neuroscience, systems biology. I felt dizzy (like a visitor to the infinite hyperdimensional library of Borges). My quest had plunged me into intellectual depths way outside of my specialty, and I couldn’t help but feel a mad tingling sensation simultaneously drawing me to dozens of books on these shelves.

“Focus, Lipschitz. Focus” I told myself. I settled for a classic Chomsky book on syntax, and a book of Polynesian mythology. I made my way back to the checkout counter, where Leopold kept watch amidst stacks of incoming books.  The proprietor peered at me over his glasses as he rang up the Chomsky book.

“Noam Chomsky, Aspects of Syntax.” He spoke in a neutral tone, but it still sounded like a question.

“Right. Well, I’m having a dinner party and I need to convince my guests that I’m an intellectual.”

He eyed me quizzically, half-smiling, some inner calculation proceeding in his consciousness. After a small delay, he replied, “This is an excellent book. I hope your guests are properly impressed. Assuming you actually read it.”

Suddenly it dawned on me that this unassuming fellow standing in front of me was the mind that had had carefully curated this amazing collection of obscure and luminous books.

“Is this your store? This place is fantastic. I’ve never heard of it – I wonder how I ended up on your mailing list.”

He looked puzzled, “I have a mailing list?”

At that moment I started to feel a little awkward about using the online BOGO coupon.

“Maybe my daughter set it up. She helps out around here from time to time.”

Anyway. “So, this bookstore is your baby? Wonderful selection. I have to ask, what’s your background?”

“Ah, well. I was once a professor of linguistics, but I dropped out of the rat race to spend more time with my studies.”

I know dropping out of academia to spend more time doing research sounds ironic, unless you’ve worked at a university. I instantly connected.

“Linguistics? You are just the man I need to talk to. Got anything for alien races beyond human conception?” Filter. Dammit. Normally I have a filter.

Fortunately, he let it go. “Does James Joyce count? I’m fairly competent at Joyce. I once developed an algorithm to discern higher order structure from syntactical patterns in Finnegan’s Wake.”

“Finnegan’s Wake? I tried reading that once. Good job finding higher order patterns in that one!”

“Well, the secret is you have to discard notions about linear word order, strict literal interpretations, and focus on rhythm, syllable length, cadence, repeating motifs, things of that sort. Really, quite a lot of it is in that book you have there.”

“Polynesian mythology? I should have suspected!” being intentionally obtuse.

His patience with me was admirable. He smiled amicably, and let it pass. “My bookstore’s name came from Finnegan’s Wake. Chaosmos. Page 118.”

“I love that word! Chaos, cosmos. Perfect.”

“It also refers to the literary device of chiasma, of which Joyce was so fond.”

Wait! I had actually heard of this one. Back in grad school when I was decompressing my brain between intense periods of scientific rigor, I would smoke pot and try to read Finnegan’s Wake. I never understood it, but it did occasionally make me giggle (which maybe meant some part of my mind understood it). At one point I bought a Cliff Notes guide to James Joyce, and read about his use of chiasma, where a phrase would be repeated in one sense, and then reversed. Sort of like Carefully Curated Books, Books from the Obscure to the Luminous, but not exactly.

He continued. “I spent a lot of time looking for hidden symmetries, like chiasma, detecting broader scale patterns in language. Global connections between repeated motifs, things of that nature.”

Something started tickling my brain. “Chiasmas. Sort of like inverted repeats in DNA.”

He raised his eyebrows.

“There are bits of DNA called transposons that hop all over genomes, they use inverted repeats to pop in and out. Nature’s chiasmas.”

“’Language is a virus from outer space,’” he quoted.

“William Burroughs. Nice… It makes me wonder if any of your linguistic techniques might be applied to molecular biology. I’ve been trying to use information theory to detect… unusual signals in DNA.”

Possibly the slightest hint of an eyeroll at the mention of information theory. “Well, I’ve done a bit of cryptography consulting work, and information theory can certainly be useful when you have no idea what you’re looking for. But I prefer a hypothesis-driven approach to discerning meaning from language. What is the message likely to contain? Is it a natural language? What is its structure? A purely statistical attack mainly generates a lot of uninterpretable correlations.”

I nodded. I certainly had my share of uninterpretable correlations. I was starting to feel a strong sense that I needed this guy on my team. “So, what’s your current research program, here at the University of Chaosmos? Now that you’ve managed to figure out Finnegan’s Wake.”

“Oh, well, I’ve always been captivated by the idea of building a BS detector. But that’s probably not practical, what with Gödel’s Theorem and all that. It would be nice to understand the essence of language and consciousness. What is truth? What is beauty? Simple questions like that.”

“You know, I did see a Chomsky quote recently about how modern science was started because people started to realize that simple things were puzzling.”

He smiled. “That’s my man.” He looked wistful for a moment. “You know, some of my students used to refer to me as Samuel L. Chomsky. This was in reference to a popular American actor, widely considered to be a bad ass.”

“I am aware of his work.”

Suddenly he dropped into his best stone-cold, bad-ass SLJ accent, “And I dare you, I double dare you, motherfucker, say ‘Colorless green ideas sleep furiously’ one more time.”

I was a speechless for a few seconds. “Huh, and so you had a hard time fitting in with academia? That’s weird.” That clinched it. He was officially on the mad science team. “So, you mentioned occasional consulting work. I may actually have a job that’s suitably puzzling for you…”

Though his taste in obscure and luminous books was impeccable, you’d have to move a lot of Chomsky to pay rent in San Francisco, even in this neighborhood. So to discover that he moonlighted as a consultant and translator made a lot of sense. Turned out he was receptive. We talked until well after his regular closing time. By the time I walked out of Chaosmos, it was a dark and stormy night.

I was close to the Wharf and the air smelled like brine, kelp and fish guts. I kept hearing a second pair of footsteps on the wet pavement, but maybe it was the rain echoing in the empty streets. Started imagining shadowy human figures in my peripheral vision, so I ducked into a hole-in-the-wall coffee shop to escape the rain and my paranoid mind. I was greeted by dingy lighting and the welcome smell of stale grease. I paid $5 for an over-brewed coffee and felt the chill gradually seep out of my skin. Through the reflections in the front window I caught a glimpse of a silhouetted figure in a trench coat and a bowler hat, and had an almost subliminal sense of momentary eye contact. I shook it off and dialed up a Lyft to the train station.

I caught the last train back to the South Bay. The train was half-filled with soggy travelers, and I could swear the faint odor of fish guts had followed us onto the train. I ecstatically collapsed into a seat, stripped off my raincoat and started paging through the Polynesian mythology book. I went straight for the sea gods. I read a little about Tangaroa, the sea god of the Maori people, sometimes taking the form of a whale. Banished to the sea after a major dysfunctional god family feud, where he spawned many sea creatures. Moved on to Kanaloa of Hawaii. Ooh, this one is a squid! God of the ocean, the underworld and magic. Lord of slimy, wet venomous things. Possibly the same deity, in cephalopod form. The myth of a scary squid god banished to the depths was not lost on some of the more scholarly fans of H.P. Lovecraft, and possibly to the writer himself, who placed Cthulhu’s sunken prison city, R’lyeh, in the remotest part of the south Pacific.  Then there was Dakuwaqa, the shark god of Fiji, who thought he was the top of the food chain until he took on a giant octopus guarding the island of Kaduva. The tentacles have it.

I noticed someone was reading over my shoulder and glanced up. A pale man of indeterminate age, a shaved head and somewhat bulbous eyes was overly fascinated with my reading material.  He gestured toward the book and spoke in a raspy voice, “Dakuwaqa. Shark god. He’s not so tough. Kumugwe is better.”

I was annoyed by the interruption, but impressed this random hipster knew about an obscure Polynesian myth. How many over-educated people were there in this city? The poor guy probably had a Ph.D. and worked in Starbucks.

“Well, yeah, he got his ass kicked by a giant octopus. Total wimp. Kumug-what now?”

“Kumugwe. Best sea god ever. Dakuwaqa was beaten by a giant octopus. Kumugwe has a pet giant octopus.”

“So, doing the math, Kumugwe is at least two levels above Dakuwaqa in bad-assitude?”

“Yeah. Plus he eats eyeballs and can see the future.”

I scanned through the index, “He’s not in here.”

“Kumugwe is from the Pacific Northwest. But Tangaroa, Kanaloa, they’re all the same god.”

“And Cthulhu, too, right?” I said, grinning.

His expression didn’t change. “This is my stop.” He grabbed his trench coat and bowler hat and strode away.

I almost deleted that email. It was such a weird, spammy address, something like 17N151W@panthalassa.net, but the seminar it was advertising caught my eye: “Using artificial intelligence to assess noise pollution and acoustical niches in the deep sea.” It was an odd venue I’d never heard of, but it was close to the beach and it didn’t take much to lure me away from campus to somewhere I could stare out at the watery horizon, even if the talk sucked.

The seminar was fascinating, as was the speaker. She was a striking Polynesian woman wearing something that some might argue could have been construed as somewhat unprofessional in terms of being kind of revealing. Personally, I was fine with it. She had used some kind of neural net software to analyze sounds recorded using the US Navy’s deep-sea recording network, mostly used to detect enemy submarines, but now sometimes made available to researchers studying underwater acoustics. Back in WWII they discovered they could send low frequencies thousands of miles along the Mid-Atlantic Ridge, where the water conditions reflect the sound waves into an effective deep sound channel. In theory, a downed pilot could set off an explosive charge in this channel and distant listening stations could triangulate his position and stage a rescue. Whales also use this low frequency approach to communicate over huge distances. But just like the sounds of birds and insects in a healthy forest, the ocean environment is crowded with sounds across the whole spectrum, from whale groans to dolphin squeaks to the chattering of shrimp. And now, add to this symphony the dull roar of myriad fleets of container ships, endlessly crossing the oceans connecting the empires of China and Walmart, along with oil tankers, cruise ships, etc. Then throw in the occasional shock wave from oil exploration ships doing seismic surveys with air guns, plus a few lethal sonic blasts from military SONAR. That’s your modern marine acoustic environment. Sorting it all out can be a mess. Dr. Kaiakea Alana had developed a neural net/machine-learning/fuzzy-logic/whatever program that could sort different waveforms into bins, some of which represented species. She overlaid onto this mosaic of acoustic niches the jarring sonic intrusions of human activity. Some sounds kill outright. But the more subtle toxic sounds disorient, disrupting communication, leading whales astray to beach themselves. In urban environments, birds change their songs to fit in with the crowded, competitive sound landscape. Will marine life be able to adapt to sonic attack? Her final message was at once inspiring and sad: if we just listen carefully, the complexity of the marine environment is revealed to us. But we need to shut the fuck up.

Her algorithm had been able, with decent confidence, to attribute some sounds to certain species, such as various baleen whales, but I noticed that there were some unidentified “bins” that included consistent sound signatures without a clear assignment to a known species. I had to ask about these in the question-answer period.

“I notice you have several unidentified bins. How do you interpret those?”

“Well, they could be previously undescribed modes of known species, new species, classified military sea craft or SONAR experiments, or some unpredicted artifact of the complex acoustic environment of the abyssal zone. Probably the latter. The sonic environment is so rich that it’s hard to filter out all the noise with complete confidence. However, statistically, the bins I presented here appear to be non-random sounds produced reproducibly in the environment, either biotically or abiotically. So short answer, I don’t know.”

Hmmm. Intriguing. I had been so focused on DNA I hadn’t even considered sound. But sound was the preferred medium of the deep sea. Light doesn’t travel well in turbid waters (though tell this to the show-off squids with all their chromatophores). Sure, maybe my beloved Abyssal Ganglia was linked through myoelectric impulses and stored Alexandria Libraries full of cultural knowledge in DNA, but what about sound? Sound carries great distances underwater and moves way faster than in air. Could separate nodes exchange information efficiently by bursts of high bandwidth vibrations? Is this more robust, more secure than electrochemical propagation through axon-like filaments of microbial tentacles? Or maybe, they just like to sing?

But her methodology was perfectly aligned for detecting a new intelligence in the abyssal zone. I had to approach her and see if she could somehow be recruited, or if I could at least steal her ideas. I waited for the break, and politely made my way through the predominately male crowd that gravitated toward her.

“That was a wonderful talk, thank you so much. I’ve just recently become interested in this topic and I don’t know much about it. I was really intrigued by the potential of your technique to detect new forms of communication. Do you think there might be sound generating creatures we know nothing about down there?”

Her eyes could have reasonably been described as oceanic and limitless.  “Oh, yes, I’m certain there are things we know nothing about ‘down there.’”

I struggled to maintain eye contact, keeping my eyes at a high altitude. It was only partly her low-cut top that made this difficult. The immeasurable depth of her eyes was also disconcerting. “Right, the abyssal zone is like half the planet. But it sounds like sound is a great way to explore it. I wonder, you’ve managed to sort out all these complex patterns into different bins, maybe different species. Is there any hope of figuring out information content from these data?”

“Well, some signals are quite repetitive, like mating calls of some fish species. So those aren’t very information-rich.”

“Right, they are probably mostly saying ‘Hey Baby, check me out.’”

“Yes, that, though maybe also some information on their size, age and gender. Cetaceans, on the other hand, seem to report all sorts of things about their environment. By listening to each other baleen whales know the position of their pod relative to major landmarks along their migratory route, like seamounts, bays, etc., so their speech changes with their location. Whereas dolphins and orcas seem to communicate in higher frequencies: clicks, whistles, chirps, and possibly “sono-pictures,” literal representations of their immediate environment. For example, their word for ‘flowerpot’ would be a sonic picture of a flower pot.”

“That comes up in dolphin conversation much?”

“It was a recent study I saw. They visualized dolphin sono-pictures for various test objects using a device they called a CymaScope. One of them was a flowerpot. Though to be honest, you really had to squint to see anything resembling a flowerpot.”

I shook my head in wonder. “Your sound clips were amazing. It sounded like the ocean speaking. So, uh, have you learned the language of Gaia?”

She became serious and solemn. “When Gaia speaks, her meaning is clear.” She spoke with enough gravity that (paradoxically) several male satellites started to leave her orbit (yes, that’s the simile I’m sticking with. Dammit, Jim, I’m a scientist, not a poet). I might have written her off as crazy, too, but she was a genius with signal processing, and I suspected that her madness might be compatible with my own.

The dissipating crowd allowed me to be a little more candid. I smiled, “Absolutely. I’d love to hear Gaia speak. It’s just that all the good feedbacks take decades, centuries, millennia, and we’re messing things up by the minute.”

She nodded. I continued to babble.

“I am working on something very similar to your project, but in the sphere of DNA. I am looking for patterns in the cacophony of metagenomic data. I believe there is life in the deep ocean that we have not recognized because it is so different from us, so alien, that we have not recognized it. And I think it may be Big and Important. It occurs to me that the approaches you are using to analyze the acoustic environment might be a perfect complement to my work. I have a bit of funding from a private donor to pursue this. If you are interested in collaborating, maybe we could talk?”

She smiled inscrutably, reached into her bag and handed me a business card, before she was once again swallowed by a wave of polite conversation, coffee and cookies.

Sensation, calculation, action.

A signal is sent. High above a chemical is released.

A nearby bloom of algae takes heed. Genes are switched on. Dimethyl sulfide is produced and wafts into the atmosphere. Gradually at first, then faster, clouds form overhead. The water cools.

Elsewhere, another signal is sent up towards the light. A distant limb releases a pulse of nutrients and growth factors. Prochlorococcus blooms, creating a dense patch of chlorophyll. Sunlight pours down onto these antennae. The water warms.

Between these two patches, air currents begin to move. Chaotically at first, then taking shape. A gyre is formed. It grows as it pulls energy from other air masses. It becomes a hurricane.

The hurricane flows over the land, washing nitrogen, phosphorus, iron, silica into the sea. Feeds life. Life takes a great breath of carbon, and rains down to the sea floor.

This is good.

Over the weeks, I gradually assembled some crude computational machinery to sift through the giant DNA database. I pulled together published metagenomes (random mass-produced sequences from the environment) from seawater, sediment and the few subseafloor crust samples that were available, and focused on the misfit sequences that hadn’t been matched to anything known.  I searched for sequences that appeared multiple times in different abyssal zone samples and eliminated the ones that were also found in a control database from terrestrial environments. These searches produced long lists of sequences that were worth a second look. Unfortunately, this literally meant me looking at sequences and trying to manually figure out what was going on. I could eliminate some of these sequences in more focused searches by matching them to known species that had already been identified in that sample. If this were a typical metagenomic project, I would have been very happy about finding these connections, as they chip away at the metagenomic dark matter. But this was just sorting the unknown into safe, comforting known packages – it was not uncovering anything truly new. I also used the SETI approach to search for messages in DNA that stood out from normal genetic code based on their information/entropy content. I ended up with a bunch of candidate sequences, though I had no guess as to their function or meaning. So far, I had not discovered the digits of pi or the prime numbers encoded in any obvious way.

At the same time, I also tried looking for signs of suspicious DNA splicing, based on the hypothesis that this creature was an expert in biotechnology. This turned out to be difficult because hopping between genomes is the most natural thing in the world for DNA. I found all sorts of “genomic islands” of mobile DNA, but most of this was pretty much the usual transposons and proviruses you find all over the genetic landscape. However, one of my searches pulled up a chunk of DNA that looked like a combination of wildly different species: a protein from an animal flanked by clear bacterial sequences. I started to get excited – even if this had nothing to do with what I was really looking for, gene transfers between animals and bacteria are rare and interesting. I ran a test to see if this was a so-called chimera that had arisen from a sequencing error, where two separate pieces of DNA mistakenly get copied into the same sequencing reaction. Crap. The search found part of this mixed sequence as an independent, normal-looking sequence in the same metagenome. This meant the odds were strongly in favor of the mixed sequence being a chimera. Oh well, a routine disappointment. I continued to toil away at this analysis, tuning the parameters a little to reduce these kinds of false positives. Not long after, the search flagged another sequence like this. I glanced at it and again, my heart sank a little: it was the same one I had found before. But wait, this was in a completely different sample. In fact, this one hadn’t even been collected by the same research team. The odds of generating the same chimera in two independent samples is pretty low. I started looking at this in more depth. It was impossible to interpret this sequence as DNA, but when I translated it to amino acids an amazing pattern emerged. Part of the amino acid sequence had a good match to a proteolipid protein (PLP) from a shrimp species, and this region was flanked by sequences that looked like bacterial lipoproteins. I followed some links to find out more about PLP. Also called myelin PLP, the dominant protein that insulates axons in the central nervous system, greatly speeding up transmission of electrical signals among neurons [12].  A brain protein in a bacterial genome?

I finally had something really good to tell my backers. I posted an update on Kickstarter:

“Still early, but potentially exciting news! Possible eukaryotic brain protein found spliced among bacterial sequences. Interestingly, GC content and codon usage are consistent over this stretch, indicating these genes were combined long ago (when new genes are acquired they gradually take on the characteristics of the new genome). The brain protein is most closely related to myelin PLP in shrimp. Incidentally, the current record holder for fastest neuronal signal is the Kuruma shrimp, clocking in above 200 m/s (about twice as fast as ours).”

I still hadn’t received a response from G. Poisson. There’s something fishy about that guy, I thought, but as long as his money’s green. However, several of the minor backers posted comments:

“Blessings upon you and your work! Soon we will know the Mind of our All-Mother, and we will bathe in the cleansing Waters of her Wisdom.”

“Dr. Lipschitz, you have shed light upon the darkest abyss. But beware, ‘for in these rays we are able to be seen as well as to see.’”

Great, my project was being followed by tripped-out Gaia and/or Cthulhu devotees. I had to snicker at the last one. It was a quote from one of my favorite Lovecraft stories, From Beyond. I started mentally riffing on these themes, “That Lipschitz should ever have studied science and philosophy was a mistake. These things should be left to the frigid and impersonal investigator, for they offer two equally tragic alternatives to the man of feeling and action; despair if he fail in his quest, and terrors unutterable and unimaginable if he succeed.” I was feeling giddy. “Watery Wisdom” is good, though personally I might have gone with “Briny Brain.” We will Cavort in the Crustacean Crenulations of Her Briny Brain. Ah, Godbless’em. Good people. They gave me money. They believe in my work. It’s wrong for me to ridicule them. Hee hee hee.

Searching for the key away from the lamppost: Exploring genomic dark matter in the darkest part of the world.

We live on a placid island of ignorance in the midst of black seas of infinity – H.P. Lovecraft

Intelligence is a highly adaptive trait. In the case of humans, it has granted otherwise mediocre creatures dominion over the Earth’s surface. Given 3.5 billion years of life on this planet, even just the 500 million years or so since the Cambrian explosion, advanced intelligence is likely to have evolved independently more than once. Evolution has produced ever-increasing complexity, punctuated by extinctions. A complex organism that has survived multiple extinction cycles could be orders of magnitude more complex than the most complex animal that arose recently. Advanced complexity allows for advanced intelligence. For example, a slime mold, resembling a mindless blob of protoplasm lacking specialized structures or organ systems, can solve complex mathematical/topological puzzles purely by the emergent properties of its network (for example creating a model Tokyo subway system that was as good or better than the original). Human intelligence is a product of the trillions of synaptic connections among the brain’s neurons. There are an estimated 10³⁰ microbial cells on the planet [1]. If some small fraction of these were properly networked, their collective intelligence would exceed ours to such an extent that it would seem godlike from our perspective.

Advanced intelligence allows skillful perception and manipulation of the world. Therefore, the hypothesized super-intelligent non-human lifeform is highly successful, and so should be widespread. Because humans have not yet discovered this widespread, highly intelligent lifeform, it must be well hidden. It is most likely to live in the least explored part of the planet, the abyssal or hadal zones of the deep ocean, and to have biological signatures that are not readily recognizable. The technology of this species must be similarly hard to recognize or detect. Therefore, its artifacts are subtle and almost indistinguishable from natural features. Environmental conditions in the abyssal zone are constant, and so an organism adapted to this environment would require no artificial shelters. Abundant energy is available in the form of organic matter snowing down from the upper layers, through geothermal energy in certain areas and from oxidation of Fe-rich basalts in the oceanic crust. Purely biological solutions exist to all aspects of life in this zone. However, to survive the cataclysms that occur at epochal time scales, an ancient, advanced intelligence would require an ability to sense and respond to its environment in innovative ways. A completely genetic technology would be highly effective and difficult to detect unless specifically searched for. Hence, a key piece of evidence for the existence of this hypothesized lifeform, and the central clue to the nature of its biology, is that it has not been discovered.

Dear reader, does this sounds preposterous? Consider the seemingly preposterous aspects of the world that you now take for fact. Our minds struggle with vast scopes of space and time, but look at the wonders that evolution has wrought given incremental changes over billions of years. This is the reason the uneducated often cannot accept evolution: the complexity that arises from simple, local processes seem fantastical to those who fail to consider the combinatorial power of countless molecules operating over deep time.  To accept the wonder of our existence, the incomparable beauty and complexity of nature, and then to scoff at the idea that we are not the sole advanced intelligence in this world, is an act of profound contradiction.

In fact, a being dwelling in a constant environment with abundant metabolic energy sources available through direct adsorption into its tissues could dispense with the excessive corporeal baggage to which we primates have become accustomed. Without the need to support itself on land, move about and hunt, there would be no need for our complex anatomy. Such a being could be almost entirely brain. A human brain is composed of about 100 billion cells, each with about 1000 interconnections on average. This capacity could be equaled by a network of bacteria-like cells in a small blob of marine sediment. Abyssal plains comprise more than half of the Earth’s surface area. The computational power of a vast, highly connected Abyssal Ganglia could dwarf that of the human mind and our computers.

Such a being dwelling in the abyssal zone could easily be missed by the patchy surveys of this vast area, especially if it harbors the innocuous form of a vast but dispersed colonial microorganism. Its genetic signatures could be similarly cryptic, given the general difficulty of classifying highly novel sequences in databases. If, as I hypothesize, this organism has evolved tools for genetic engineering and has developed a purely biology-based technology, its molecular signal would be far too complex and variable to recognize with current bioinformatics approaches. However, the paradoxical hyperdiversity associated with the deep sea [2] may provide indirect evidence for such a technology. Could this diversity be an indicator of willful genetic experimentation? The Candidate Phyla Radiation (CPR) is a diverse cluster of marine bacterial phyla presumably symbiotically associated with unknown marine hosts [3]. Many of these phyla could represent the carefully curated components of the Abyssal Ganglia’s machinery for capturing energy from the environment. Furthermore, the novel “fourth domain” gene families found in marine DNA could represent this organism, or the impacts of its technology [4].

Of course, diversity is the very hallmark of biology, and the above patterns, while intriguing, can be explained without invoking intervention by an advanced intelligence. Furthermore, these observations were based on extensions of mundane biology, for example surveys of ribosomal RNA genes or analysis of conserved gene families that reveal novel variations on familiar themes. What might we find in the abyss if we searched for an entirely outré form of biology? (A lifeform completely alien to us, though in some ways more fundamental to the Earth than humans, spanning the planet when our ancestral cells had scarcely become multicellular).

Modern DNA sequencing platforms are churning out petabases (10¹⁵ nucelotides) per year of new sequences [5]. Though much of this is devoted to the vain and redundant task of glorifying the human genome and our excreta (also known as the Human Microbiome Project), massive amounts of environmental metagenomic data are also generated from soils, sea water, ocean sediments, animal feces, and the slimy, microbe-coated surfaces of myriad creatures. These samples show us that the microbial diversity of the planet is, for all practical purposes, inexhaustible. Easily half of this DNA is unrecognizable, and relegated to the classification of “genomic dark matter,” an allusion to the matter that makes up the majority of the universe and whose gravitation is largely responsible for holding together spinning galaxies against their centrifugal force, but is invisible and uncharacterized. Routinely, researchers dwell solely in the well-lit segment of this pie chart, where homologies to known sequences allow the discovery of marginally novel species, and the tracking of known species across space and time. This is the proverbial “looking for the key beneath the lamppost.” But the secrets I seek do not lie here. Evidence for my hypothesized life form, the Abyssal Ganglia, will only be found in the genomic dark matter of the darkest, least explored regions of the planet.

Large international efforts, such as the Census of Diversity of Abyssal Marine Life (CeDAMar), the International Ocean Discovery Program (IODP) and the World Register of Marine Species (WoRMS) [6], have begun to collect water, sediment and subseafloor crust samples from the deep sea. Metagenomic sequences for some of these samples already exist, and many more samples have been archived, and may be requested by serious researchers. Therefore, my initial exploration of this eldritch abyss will be virtual.   In this proposal, I enumerate hypothesized properties of the Abyssal Ganglia, the genetic signatures yielded by these properties and bioinformatic strategies for detecting these signatures.

Phase 1 of the research will focus on preexisting abyssal zone metagenomes to optimize the search parameters for Abyssal Ganglia signatures. Phase 2 will expand the search for these signatures and create a spatially-explicit model for the distribution of this organism. Phase 3 will involve hijacking a deep-sea submersible and confronting the central hub of this Leviathan in the murky depths of the abyss.

I hypothesize that the Abyssal Ganglia is ancient, highly intelligent and exceedingly well-adapted to its environment, and will therefore be widespread in the abyssal environment. Having thus far escaped detection, its genetic signature will lie within the realm of unidentified sequences. Therefore, I will search for recurring patterns that are common in the abyssal zone, are not found elsewhere and are unrelated to any known sequence. These patterns may be identified in DNA sequences, or in higher order geometric or logical patterns that arise from non-conventional analyses of DNA sequences.

As the Abyssal Ganglia is hypothesized to be highly intelligent yet no artifacts of its technology have been discovered, it is hypothesized to have a purely biological technology, which produces no conspicuous artificial structures but leaves its signature in DNA sequences. One consequence of this technology would be an abundance of chimeric genes or pathways, which show signs of splicing from distantly related organisms. These will be detected using modifications of existing software that search for chimeric sequences that arise during errors in DNA sequencing, except the hypothesized sequences will arise identically multiple times in independent samples. Gene splicing will also be detected as discontinuities in nucleotide and dinucleotide signatures [7], reflecting regions from divergent source genomes. These approaches will require long assemblies of sequence reads that lack a known genomic scaffold. This challenge will be overcome using k-mer frequency binning methods to assemble non-overlapping contigs without relying on homology to sequenced genomes [8].

The second consequence of a highly intelligent organism with advanced DNA editing technology could be non-conventional signals encoded in DNA sequences. This approach borrows from the Search for Extraterrestrial Intelligence (SETI) that have developed algorithms for detecting “beacons” (intentionally transmitted information) by analysis of information content in astronomical data [9]. For example, the Abyssal Ganglia could back up its network structure as a DNA sequence. It is hypothesized that this organism stores information in the combinatorial connections among its cells, analogously to the human brain. It would be highly advantageous to store a coded image of the network structure in case of catastrophic loss.  Such a mind could also have other uses for expressing numbers and mathematical expressions, which could also be stored or transmitted in DNA form. Sequences derived from an organized array of non-random numbers would have lower entropy values than typical sequences that code for ribosomal RNA or proteins. Based on my models of numerical information storage in DNA, highly regular sequences could even be distinguished from known repetitive sequences found in genomes (Figure 1).

Having identified candidate sequences for numerical (or alphabetical) content, specific decryption algorithms can be deployed. The identification of such codes by relatively low entropy content implies that they are not securely encoded, or else such signals would be indistinguishable from random noise. Therefore, there are a finite number of logical numerical systems based on the genetic code (i.e., base 4 using A, C, G and T nucleotides to represent 0, 1, 2 and 3). It would be a straightforward task to search for known numerical sequences (e.g., the integers, pi, the Fibonacci series, the primes) by trying permutations of base codes (mappings between {A,C,G,T} and {0,1,2,3}) and word length (number of bases used to represent each number). A simple exercise with this approach shows no exact matches greater than 24 bases to these numerical sequences in GenBank (Table 1). This is not surprising, as this database contains only the genomes of known organisms and environmental surveys of known genes. A long numerical sequence found in metagenomic dark matter of the abyss would clearly indicate an encoded signal with an astronomically low chance of arising randomly.

 

Calculating the information content of DNA sequences could indicate the presence of intentional signals. However, a deeper metric of intelligent life would be the computational complexity of this system. Just as the information content is related to the number of possible discrete states that can be recognized in a message, the computational complexity arises from the number of distinct internal states of the computational system. Life, and in fact all of nature, can be thought of as a Turing Machine that reads data from its current state, performs operations on these data and outputs a new state. In other words, the life machine senses conditions and responds to them, causing the system to evolve, or as eloquently put by Crutchfield (2012), “We posit that any system is a channel that communicates its past to its future through its present.” The number of possible ways a system could respond to a set of inputs gives rise to computational complexity. Just as most DNA sequences tend to have intermediate information content, balancing between randomness and predictability, the computational complexity of biological Turing Machines appears to be balanced between chaos and order [10]. A complete description of the computational complexity of the Abyssal Ganglia requires a full understanding of its natural history and biology, requiring not just DNA sequences, but how the entire system changes over time (including, but not limited to, gene expression). However, a more limited and feasible approach based on available data is to analyze DNA sequences as complex dynamic systems, inferring new states that can arise from previous ones, linearly, as a sequence is read from 5’ to 3’ end, or non-linearly, among clusters of related sequences found in the same sample. This approach could reveal higher order patterns not detected by the other information theory approaches described above.

These preliminary analyses will allow the optimization of search methods and identify potential signals of intelligent life in the abyssal zone. This search will then be expanded to include samples that have been collected and archived, but which do not have adequate DNA sequence coverage. Samples will be requested and sequenced deeply. However, only a tiny fraction of this environment has been explored, and particularly large gaps exist for the central Pacific and the Southern Ocean. To quote Stuart et al. (2008), “Attempting to understand abyssal biodiversity from existing data would be tantamount to characterizing terrestrial plant diversity based on 1600 random snapshots of plant life in, for example, only continents of the eastern hemisphere.” Therefore, the second phase of research will be to collect new samples based on spatial patterns descried from existing data. In the absence of a clear clustering of positive signals in the initial data set, new samples will be collected according to a golden spiral search pattern centered on locations with the clearest positive signals from phase 1 (Figure 2). Data from this mission will be used reiteratively to design new sampling transects to identify the epicenter of these signals, and ultimately, to locate a central hub of the Abyssal Ganglia. The experimental details of phase 3, in which a deep-sea submersible is commandeered by a small ragtag band of free-thinking scientists against all odds, is beyond the scope of this current proposal.

After weeks of trepidation, mixed with partially suppressed hope, I saw the message in my inbox.

I regret to inform you that the National Science Foundation is unable to support your proposal referenced above. Your proposal was reviewed in accordance with the general merit review criteria established by the National Science Board that address the intellectual merit of the proposed activity and its broader impacts…blah blah blah you lose. Again.

The familiar sickness, a punch in my gut. Festering disappointment from years of these form-letter rejections, rising up into bilious rage. I didn’t even read the reviews. I didn’t need to. I’ve seen all the variations. Arbitrary criticism of technical details. Too ambitious. Too risky. Not a first order problem. Not Transformative. Assholes. They want transformative? Fine.  No more half-assed proposals, logically extending previous research in bite sized increments. Time for revolution. Time for me to stomp on these mental midgets.

My mind lashed out with all its strength against the rigid, imagination-challenged, mundane and mediocre, puny and pedantic intellects that had denied me. Rage, disgust and pride blazed across dormant neurons, igniting a plasma of synapses. I feverishly hypothesized, speculated, reasoned, drawing together everything I knew about life on earth, connecting a maelstrom of ideas that would seem absurd to a conventional (sane?) scientist. I was outside the box. Leagues beyond the predictable machinations of the scientific orthodoxy. When the complete concept finally crystalized out of this electrified brine of supercharged mental activity, it was so compelling, so parsimonious, so beautiful, that I had no doubt that it must be true.

I know. It sounds pompous and poetic, but it seemed like a really good idea at the time. Even as I sit here wondering whether I’ve hastened or delayed the demise of human civilization, I can’t help but feel proud that I thought of it first. Kind of. They say there’s nothing new under the sun, and that may or may not also apply to the abyssal zone of the ocean. My idea was sort of a cross between Lovelock and Lovecraft. But did either of those guys develop a detailed experimental framework to test for the existence of a vast ancient being with god-like intelligence, so alien to our normal conception of biology that it has escaped detection, even in this age of filthy rich narcissists with deep sea submersibles and DNA-sequencing yachts?

No, they did not. Sometimes I answer my own rhetorical questions. Does that make me a monologuing Mad Scientist? Possibly.

Anyway, I wrote the proposal. I needed the emotional and intellectual release. Of course, I didn’t bother submitting it to a federal scientific funding agency. On one hand, they would never fund it, and on the other hand, someone might read it and realize that I am not actually insane, and try to steal my idea. No, I needed preliminary data before I could even breathe a word of my theory to anyone. There are already petabases of DNA sequences dredged out of the ocean and dumped onto public servers, with over half of the data ignored summarily because it doesn’t match any known genomes. Unfortunately to look for the patterns I suspected, I was going to need some serious supercomputing time, along with an assload of high throughput sequencing, and neither of these are cheap. What recourse do passionate scientists have, when continuously frustrated by hopelessly oversubscribed funding agencies? Some resort to Kickstarter. (In case you’re somehow reading this after civilization collapses, this basically amounted to begging for money on the internet). I decided to disguise the idea as a novel approach for analyzing metagenomic dark matter, the hidden majority of unidentified sequences lurking in the DNA databases, for the purpose of discovering new domains of life.  As a reward, I offered to list my backers’ names in the acknowledgements section of the resulting publications. Unsurprisingly, the results were pathetic. Other people were doing this already. What was my hook? I decided to show a bit more of my hand. I proposed to search for sequences that showed signs of symmetry and order resulting from systematic self-editing. Signs of DNA modifying itself in a directed way. How to sweeten the pot for the backers? Your name in the acknowledgements PLUS full color reprints of all publications including special supplemental information with an oversize fold out poster of the money-shot figure (Boring science paper: the director’s cut)!

Again, miserable failure. After 30 days, I had received a handful of small pledges, probably from creationists mistaking my subject for intelligent design. The NSF hates me, and so does the internet. It suddenly occurred to me I was treating the general public like a scientific funding agency, making the same mistakes as always. Careful, incremental science. Where was the fuck-you attitude that inspired the true shadow project behind these Kickstarter campaigns? It was time to put the whole thing out there. I don’t know why I was worried about someone stealing my idea in the first place – This idea was so far beyond the cognitive dissonance threshold of any reasonably trained scientist that it would be virtually invisible. I no longer cared about looking like a crackpot. This is the internet, after all. I uploaded the full proposal, in all its manic glory. “Xenobiology of the Abyssal Zone: Pattern Recognition for an Advanced Purely Biological Civilization.” Backers above the $100 level will also receive a special behind-the-scenes report on the Making of the Thing I’m Doing. Finished setting up the new campaign around 2 am. Blearily, I stumbled off to bed.

“Someone is messing with me.”

I stared in disbelief. I had set my goal at a modest $10,000. Peanuts as far as science budgets go, but hopefully enough computing time to maybe produce some convincing preliminary patterns. The total stood at $511,420. Several small donations, and based on the analytics, probably mostly from sci fi fans who mistook my project for an ambitious work of fiction masquerading as science, breaking the fourth wall and all that. And a single donation of half a million from one Gabriel Poisson. The good news, even without this joker, I had met the goal. A paltry sum that couldn’t even begin to address all the ideas I had raised in the proposal, but still, an excuse to work on the only scientific project that mattered to me. I had spent the past months muddling through the public databases with the limited resources at my disposal, in the spare time I had available between teaching classes half-filled with sleepwalking students, attending pointless meetings with whiny, myopic faculty and sheepherding lackluster graduate students toward dead-end careers. In the evenings and weekends, when I wasn’t too depressed, tired or drunk (and sometimes even when I was), I would plunge into the chaos of the public database and tap away at the rebar-reinforced concrete wall of genomic dark matter with the tiny hammer of my feeble programming skills. (Don’t get me wrong – I am a brilliant and creative scientist, but I know my limitations. I was out of my depths with this project, but that was the point. To do something this revolutionary would require me to transcend my limitations, by sheer will power, if necessary. However, I would also accept dumb luck).

And dumb luck it was. I went ahead and launched the project. I was deeply agitated, assuming Poisson was a fraud, but unable to completely suppress belief that a mysterious benefactor had recognized my genius. This latter thought filled me with a secondary source of agitation, that maybe I was the fraud, and would now be responsible for delivering something really big. So I spent the next few days waiting for the funds to transfer, planning on spending the $11k, but also half-planning for the contingency of spending $500k. Spending half a million is easy. I could have easily written a budget for $5 million, even without the 50% overhead my University normally charges. You’d be surprised how fast science funding goes. Salaries, sequencing, supercomputing, major equipment, lab supplies, ship time. The hard part would be figuring out which 10% of the project to fund.

Ah, it’s so hard to break these numbdane academic habitual anxieties, engrained from years of playing an absurd game whose rules are half clear at best. A great intellectual step! I jump out of The Box! I reject the hegemony! And then I scurry back to my desk to do the paperwork. Alor, Monsieur Poisson, I humbly accept your most generous offer, and vow to blow your froggy-fishy mind with magnificent results:

Let us plunge headlong into the gulf, heaven or hell it matters not! To find something new in the depths of the unknown!

Yeah, that was my attempt at quoting Baudelaire – I got excited for a minute. Finding half a million dollars in your bank account will do that.

 

PREVIOUS

NEXT

And now, there is a scent of extinction drifting down from above
An unwholesome warmth creeps along the benthos
Like the other great times of dying,
But this time is different.

Among the legged ones,
There walks a seven-billion-brained beast
The soundscape has become noisome with thunderous blasts,
And an omnipresent grating drone
Drowning out the delicate songs of life

Across the basins, strands of a new, alien network
Pulse with information
Almost senseless
An incoherent chatter of voices in broken languages

In the cacophony there are clear voices
In the tangled futures, there are preferable paths
Invisible appendages vibrate the subtle strings of an incomprehensible harp
This is their song.

PREVIOUS

NEXT

Either you repeat the same conventional doctrines everybody is saying, or else you say something true, and it will sound like it’s from Neptune.

-Noam Chomsky

In the great scope of Earth’s history, even just the last six hundred million years, with complex multicellular life abounding, couldn’t there easily have arisen and fallen an intelligent civilization? Not mammalian, in fact, most likely marine, given how easy to hide in the depths, and how low the chance of relics surviving and being discovered. For example, the Squid People: convergent evolution has produced eyeballs, ganglia and complex social behavior unlike our own in structure, yet somehow equivalent. Even more intriguing, the great deep-sea microbe mind, the Abyssal Ganglia. A network of cells that spans the world’s oceans, tapping geothermal energy and acting as a unified global intelligence, even capable of Gaia-like actions: able to manipulate climate via DMS, the rate of C burial or even altering geothermal/tectonic activity. Perhaps the Abyssal Ganglia has the Knowing of the Three Times, and is master of natural history, using viruses to sculpt the destiny of species, ecosystems, the whole of the watery sphere. How will she respond to the threat that humanity now poses? Will she come to our aid and slow climate change, or rather decide the best course is to eliminate us so that the planet may live?

Such a being is not only plausible, in fact inevitable, given the span of Earth’s history and the forces of evolution. A purely biological technology would be virtually impossible to detect from our human perspective.

A frustrated professor, after learning the latest in an endless stream of grant proposals has been declined, is inspired to prove something so revolutionary it will dwarf the tiny minds and careers of the myopic review panels. He assembles a team of interdisciplinary researchers*, aided by a mysterious private donor (a probable tentacle-puppet of the Abyssal Ganglia**). Their voyage of discovery will lead to the terrible truth of Mankind’s Destiny.

* including a smoking hot marine biologist who inexplicably always wears a wetsuit or a bikini.

** something fishy about that guy, but as long as his money’s green

-First scribbled in June 2016 (Kilpisjärvi, Finland)

PREVIOUS

NEXT

Critics rave for The Abyssal Ganglia: Tentacles of Gaia

“Combines the thrill of a science textbook with the intellectual stimulation of a faculty meeting”

“Pedantic Beyond Conception. The aborted fetus-lovechild of Lovecraft and Lovelock”

“The story of a frustrated scientist becoming a frustrated writer.”

“A diseased mind force-fed on university education vomiting out his profoundest fantasies”

“Not enough weird tentacle sex to get you off, just enough to be gross.”

“Almost as fun as a Wikipedia binge.”

“Deep shit!”

NEXT