Gut Feeling

A sci-fi short story first written in December 2015.

Lucy opened the fridge and pulled out the dark brown bottle, shaking it gently to hear the capsules inside rattle. She unscrewed the lid, tipped up the bottle and emptied a couple onto her palm. Rod-like capsules, pale brown in colour. They looked ordinary, benign – like any other run-of-the-mill probiotics you could buy. But Lucy knew these weren’t ordinary. Each capsule contained billions of bacteria, a strain she had developed. Lucy felt a stirring of butterflies in her stomach; this feat of genetic engineering was tremendous.

It was only a few decades ago that scientists had begun to realise the profound impact of microbes on humans. The first clues came with the observed correlation of mental illnesses and obesity with gut microbiota. Then scientists found “the second brain” – 100 million neurons lining the human gut, forming the enteric nervous system, connected to our brain via the vagus nerve. But this wasn’t a one-way connection. Biochemical signals from the gut and its bacterial inhabitants were affecting the brain.

Research into the human microbiome boomed. From influencing our physical and mental health, to our behavior and personality, our bacteria seemed to be an omnipresent, insidious force that had crept into every facet of our being. With symbiotic microbial cells outnumbering human cells ten to one, scientists began to ask questions about how “human” we actually were. The answer: no longer was a human a single organism. We were walking, talking ecosystems, each of us home to a population of single-celled species as unique as our fingerprint.

Lucy was captivated by this idea. She had grown up during an exciting period of scientific advancement, and wasn’t constrained by outdated concepts of humans as autonomous individuals. In Lucy’s mind, the ability to alter your microbiome offered limitless possibilities. Why perform complex neurosurgery when you could produce the same effect via the gut? The concept was straightforward enough in theory: with detailed knowledge of the biochemical pathways in the brain, you could genetically engineer bacteria to produce a specific cocktail of neurotransmitters. By administering these bacteria with an oral probiotic, you could influence the biochemistry of the brain. She dreamt of boosting memory and enhancing intelligence.

But she no longer had to imagine. With this simple pill Lucy held in her hand, it would be a reality. Lucy had tested her treatment in mice with promising results. Her latest experiment involved tracking the neurotransmitters in real-time as they travelled from the gut to the brain. She used protein biomarkers which fluoresced green, blue and red when they bound to the tiny but powerful neurotransmitters. Lucy felt a warm glow of pride radiate from her abdomen the first time she saw the colourful fluorescence illuminate. Her very first human trials were just around the corner. If successful, the consequences for mankind would be spectacular – it would usher in a new era of creativity and progress in science.

Lucy snapped out of her daydream. She returned the probiotics to the fridge and entered a glass-enclosed corner of the lab. A warm yeasty smell permeated the air – bacterial broth freshly mixed. She spent long hours in the lab and she liked it best at night when the lab was quiet, so she could think. She felt less pressure without the suspicious eyes of her labmates examining her every move. Sometimes she noticed them reading her lab book, or examining her experimental set-up closely. It made her uncomfortable, so she tried to avoid the busy times of day. Lucy felt an affinity for her bacteria and she raised them with great care. She watched the tall conical flasks swirling in the incubator. The shaking platform inside the glass case whirred and the brown liquid inside the flasks sloshed to and fro.

Behind Lucy, the glass door slid slowly open. A gentle whooshing as a draught entered alerted Lucy and she froze. Who else would be working this late?

“Hello, Lucy.”

It was Martin, the lab leader. Lucy turned slowly to face him. Martin was short and stocky, with horn-rimmed glasses and a cardigan slung over his shoulders. She didn’t particularly like Martin, who had an air of superiority and an egotism that didn’t sit well with her. He spent most of the day in his office talking loudly and guffawing with the other “old boys” who still occupied the upper echelons in chemistry. Progress for women in Lucy’s field had come more slowly than others. Nonetheless, Lucy tolerated Martin because his lab was well-stocked and he gave her a great deal of freedom in her research.

“Hello, Martin.”

Lucy noticed the bottle of acid in Martin’s hand and she felt her stomach butterflies flicker – an unpleasant, foreboding flickering.

“I’ve been following your progress Lucy, and I have to say, I’m very impressed. You’ve got further than I expected with this project.”

“Thank you.”

“You’re quite welcome. But I have some bad news Lucy. I’m afraid I can’t allow you to continue with this avenue of inquiry any further.”

Lucy frowned, taken aback. “But why? I’m so close. I don’t understand.”

“You see Lucy, you’ve gotten a little too far for my liking. Your intentions for this technology don’t really, ah, gel with my vision.”

Lucy stared, speechless. Her intentions had been nothing but noble.

Martin continued, “I like the premise. An oral probiotic to alter the mind. So simple and elegant. Brilliant, even. “

Martin flung the open bottle of acid at Lucy’s face and she recoiled in excruciating pain as it burned her face and chest. She collapsed, writhing on the floor. Martin turned to the conical flasks whirling madly in the incubator. His lips contorted into a smirk.

A few mornings later, Martin sat in his office and opened the local newspaper. In the corner of page five was a brief article.

“Scientist injured in lab accident.

Dr Lucy Johnston, scientist with Labrax Pharmaceuticals, was in an accident last week while working late at the Labrax Laboratory. A chemical spill, involving highly corrosive hydrochloric acid, occurred at about 11pm. Dr Johnston’s colleague, Professor Martin Bourke, was in a nearby office at the time and was able to call for medical assistance. ‘This is a terrible accident and all of us here at Labrax wish Dr Johnston a speedy recovery. The company will be doing everything possible to assist Dr Johnston, including taking care of her medical expenses,’ said Professor Bourke. Dr Johnston is said to be in a stable but serious condition at a private hospital. The Health and Safety department of Labrax Pharmaceuticals is investigating the incident.”

Lucy awoke in a daze. Her face was covered in bandages, save for a slit for her eyes. From her restricted view, she could see a hospital room – all white, sterile with glaring fluorescent light. She tried to move her arms and legs but they were restrained. Her mind felt fuzzy, black and white static.

Crisp footsteps signaled the approach of someone, but she couldn’t see. A hand gently moved the bandages near her mouth, and pressed a rod-like capsule between her lips. She swallowed.

Martin entered the room and addressed the white-coat-clad person tending to Lucy, “How’s our subject coming along?”

“Excellent. She really had done a fantastic job – just a few tweaks to genes here and there and we’re fairly certain we’ve got a product capable of altering thoughts. The trials this week will confirm we have established control.”

Martin felt an anticipatory fluttering in his stomach. Why settle for advertisements and pop culture to influence psychology, when you could so easily get right at the brain itself? He imagined controlling vast populations using mere suggestion. The consequences for the elite of mankind would be spectacular. It would usher in a new era of power and wealth. Soon, he’d no longer have to imagine.

Do fish vomit?

First written in October 2013. Guest blogger Lachy joins me to explore the fascinating world of fish. We wrote this piece for a science communication class.

Fish are friends, right? Yes they are. But unlike our human friends, we don’t know some basic things about them. So in order to get to know our aquatic acquaintances better, here’s three things we’ve wondered about recently.

1. Do fish vomit?

Inspired by this incredible Youtube video of cats puking to a techno soundtrack, we wondered, do fish vomit? With his usual “I know everything guys” approach, Lachy immediately claimed that vomiting is a function all vertebrates must have. Ellen, being skeptical of such a presumptuous claim, used her impressive googling skills to uncover the truth behind this piscine puzzle.

BLARGHARGHABLARG.  Image by Maya/Flickr (CC BY-NC-SA 2.0).

BLARGHARGHABLARG. Image by Maya/Flickr (CC BY-NC-SA 2.0).

It turns out, fish can indeed upchuck their lunch. However, Lachy’s assertion that vomiting is a behaviour common to all vertebrates isn’t correct. Rats can’t spew!

2. What happens to fish in space? 

Image by Airport_Whiskey / Flickr (CC BY-NC 2.0).

Image by Airport_Whiskey / Flickr (CC BY-NC 2.0).

Living on Earth has its upsides. Literally. We (almost always) know which way is up or down. But in space, up or down doesn’t even exist! This can make life hard for creatures when they get sent to space by meddling astronauts. Lachy has seen a Youtube video of pigeons in zero gravity, and they really struggled. So what about fish in space? Would Dory be able to “just keep swimming?”

Hypothetically it could be very hard for fish. They stay upright in our oceans because of buoyancy: the force of gravity acts more strongly on the water around them than on themselves. So in space, they might just float around randomly, unable to control their movements or swim at all!

In 1973, this mystery was investigated in the Skylab. Two “mummichog” specimens were observed to dive incessantly, resulting in circular motions “as if stuck to the hands of a clock.” This phenomenon is called “looping.” But after a few days,  the mummichogs stopped such weird locomotion and began to swim normally, with their backs oriented towards the cabin’s light source.

3. Do fish feel pain?

If you’ve ever gone fishing, you’ve probably seen fish writhing as they are reeled from their watery homes, hook embedded in their mouth. Are these poor creatures in pain? Battles have raged in both the scientific literature and public court of opinion over whether fish can feel pain. But the most recent study, conducted by an interdisciplinary team of neurobiologists, fishery scientists and behavioural ecologists, concluded that fish do not feel pain the same way humans do.

Studies claiming fish can feel pain have relied on interpreting fish behaviour. But fish lack the part of the brain that perceives pain in humans, and administering painkillers, such as morphine, produces no effect on them. This suggests fish can’t feel pain, but either way it doesn’t make sense to decipher the meaning of fishy behaviour from a human perspective.

Searching for life out there

First written in April 2013.

In another triumph for NASA’s Kepler mission, two new planetary systems have been discovered. While such a discovery is not really a rare event anymore – 137 new exoplanets were found last year – a couple of factors make this finding particularly noteworthy.

First of all, some of the planets are “Super-Earths” – that is, they’re not too much bigger than our home planet. One of them, Kepler 62f, has a radius only 40% larger than that of Earth. What’s more, it is postulated to have a rocky composition.

Secondly, three of the planets are located in the so-called “habitable zone.” This is the region surrounding a star in which a planet could theoretically have liquid water on its surface. One of the planets, Kepler 62f, is the closest in size to Earth ever discovered in a habitable zone. Another, Kepler 69c, orbits a star that belongs to the same classification of our sun (G-type). Kepler scientists claim this is “a significant milestone toward finding truly Earth-like planets.”

Artist’s impression of Kepler 69c. Image via NASA Ames/JPL-Caltech.

Artist’s impression of Kepler 69c. Image via NASA Ames/JPL-Caltech.

While Earth-like planets seem like a logical starting point for our quest to find extra-terrestrial life, restricting our search to such a narrow range of environments may in fact be unnecessarily limiting.

There are many other factors to consider when it comes to deciding whether liquid water can exist on a given planet – from atmosphere, to stellar radiation, the age and type of the host star and of course an origin for water. Conversely, it is possible that environments conducive to life as we know it exist outside habitable zones – in fact, there is one such potential environment in our own solar system. Jupiter’s moon Europa is hypothesized to harbor a subsurface ocean similar to the deep oceans of Earth. The likelihood of this was bolstered recently with the discovery of an “unidentified and unclassified” bacterium in a lake buried under kilometres of ice in Antarctica, an environment postulated to be similar to that of Europa.  Effects ranging from volcanic activity to planetary mass can facilitate conditions beneficial to life, and it is also possible that life may originate on a planet that starts in the habitable zone, but then ends up outside it.

Europa. Image by NASA/JPL/DLR.

Europa. Image by NASA/JPL/DLR.

The existence of extremophiles on Earth suggests life can arise in a diverse range of conditions – on Earth it can exist in volcanic vents and nuclear waste! The resilience of life is epitomized by tardigrades and bdelloid rotifers, peculiar organisms which are extremely resitant to harmful radiation and extreme temperatures. Tardigrades have even been shown to survive in the vacuum of outer space. A couple of other factors suggest that life may be more resilient than we expect: organic molecules are able to exist in the interstellar medium, despite the inhospitable radiation. Additionally, geological evidence suggests that life appeared early in Earth’s history – perhaps as early as 3.85 billion years ago. Earth back then wasn’t like Earth today: it was hot, with a toxic atmosphere of carbon dioxide, ammonia and other gases, and a multitude of volcanoes. Despite this seemingly uninhabitable environment, life managed to emerge.

Tardigrade. Image by Bob Goldtsein and Vicky Madden (UNC Chapel Hill) (CC BY-SA 3.0).

Tardigrade. Image by Bob Goldtsein and Vicky Madden (UNC Chapel Hill) (CC BY-SA 3.0).

The border between living and non-living is blurred, and exactly what constitutes a living being is a contentious issue. Biology has traditionally characterised life as matter that is able to metabolise, grow, respire and reproduce – but this definition is arbitrary and also problematic, as it leaves entities such as viruses in a grey area. Viruses possess genes, utilise natural selection and reproduce via self assembly, however they lack cellular structure, metabolism and cannot reproduce independently. These perceived shortcomings preclude them from the ranks of living things. Our definition of life has been inconstant, and has transformed over time. For example, the invention of the microscope opened up a whole new world of microbial life to human understanding. However, redefining life might not solve this problem  – because definitions refer to words and meanings, which are inherently flexible and dynamic. What we need is “an adequately general theory of living systems” and this requires expansion of our conception of life beyond what we observe on Earth. One such theory has been proposed already, in which life is described as “the activity of a biosphere,” where a biosphere is a “highly ordered system of matter and energy characterised by complex cycles.” The originators of this theory, Feinberg and Shapiro, hypothesise that the minimum requirement for life is simply an entropy gradient (change in amount of disorder over time).

If we take Feinberg and Shapiro’s theory to be true, we can imagine that life might evolve in exotic places, such as the atmospheres of giant stars or on the surface of neutron stars. Of course, the kind of life that could survive in such extreme environments would be light years from our current notion of life – perhaps so much so that we might be unable to recognise it. In a similar vein, the human mind is unable to comprehend shapes in four dimensions, so it is entirely possible that bizarre forms of life occupy higher dimensions inaccessible to us. For example, in Greg Egan’s Diaspora, giant growing carpets composed of carbohydrate building blocks in shapes like Wang tiles appear one-dimensional but when Fourier-transformed, reveal an incredible “thousand-dimensional frequency space” rich with life. It’s all pretty mind-trippy stuff.

Tessellating Wang tiles. Image by Claudio Rocchini (CC BY-SA 3.0).

Tessellating Wang tiles. Image by Claudio Rocchini (CC BY-SA 3.0).

Returning a bit closer to home: maybe there are multiple biosystems on Earth that remain hidden from us, so-called “shadow biospheres.” Massive portions of the Earth remain unexplored – like deep within the soil – which represent potential locations for life founded on alternative biochemistry or physical processes. For example, life might be based on silicon instead of carbon, or differing chirality. Perhaps even life based on weak forces like Brownian motion might exist. Another interesting point to consider is whether life can only exist in baryonic form – that is, in the form of matter we can detect. Some cosmologists predict that baryonic matter only comprises 4.6% of the total mass density of the universe – the remainder consists of dark matter and dark energy. Maybe some form of life extends into these dark realms of the universe.

Overall, while it may be especially important to humanity to find extra-terrestrial life similar to us, I contend that any discovery of life beyond our own planet would be equally as extraordinary, and potentially more mind-blowing and enriching. Therefore I believe we need to let go of our obsession with the “habitable zone,” and think more outside the box when it comes to the notion of life.