Tag Archives: Biology

Beyond the Pale Blue Dot

In all the gin joints, in all the world…

An old movie line, but it speaks a truth: life is miraculous to the point of being impossible. We search for it. To be fair, we’ve really only begun looking seriously in the last thirty years or so. The discovery of the first confirmed exoplanet in 1995 propelled us into the heavens, and we began to seriously believe we may just find life out there. Why not? That isn’t a scientific response, but life is incredibly improbable. The amount of unbelievable coincidences that enabled life to appear on our blue green marble almost beggars belief. Everything had to be just right, or life just never would have happened. Just like the proverbial bowl of porridge, which actually leads to the topic of this post. A certain famous little girl of fairy tale fame lent her name to the region around a star at which liquid water can exist in a stable form on the surface. More precisely, this region, or “Goldilocks Zone” is the distance from a star: the sweet spot where liquid water exists. To be more precise again, the Goldilocks zone is a function of stellar luminosity and output. The more energetic a star, the further out it’s Goldilocks or habitable zone is. It’s a fairly linear progression: the hotter the star, the more distant it’s habitable zone. Image: NASA/JPL Extremely simplistic, but that’s us in a nutshell. We happen to be just the right distance from our sun. Because life has only been found here (as far as we’re aware), we naturally think that life will tend to favour “earthlike” conditions somewhere else. That probably makes some sense. However, does all life in the universe necessarily exist on a rocky, watery world that essentially mirrors our own? It doesn’t have to be the case. Much recent thinking has been directed towards redefining the habitable zone. Our solar system is one of countless billions estimated to exist in our galaxy alone. As researchers discover more exo-solar systems seemingly every day it’s becoming apparent that perhaps our particular corner of the block is actually quite unusual. For astrobiology to have any relevance at all it’s important to think outside the square. For that reason we take a look at the habitable zone as we know it and stretch it’s limits.

The Local.

In our solar system we see a complex family of objects, all held together loosely by gravity. Many of these planets are suspected to possess water. Lots of it. In fact it’s believed by many researchers that the amount of water in the solar system not situated on earth is quite large. Our blue green marble is actually fairly arid compared to many other worlds in our solar system. The Galilean moon Europa is smaller than earth’s moon, but may hide two to three times more water than is found here! Earth is surprisingly dry compared to tiny worlds such as Europa, with the blue orbs representing an approximate comparison of each world’s respective water content. Europa is one of a small group of worlds in the solar system that have piqued the interest of astrobiologists over the years, as they are believed to possess certain sets of conditions and environments that could be conducive to the presence of life. Not just habitability (as was possibly the case with our Moon), but abiogenesis. Life arising from whatever hidden firmament lies within their icy depths. The reason these worlds give astrobiologists hope is that (quite naturally) exo-solar systems come in all shapes, sizes and flavours. Moons like Europa, Enceladus, or even now quite dead worlds such as Venus and Mars throw us tantalising glimmers of hope that Earth based life is not alone in the universe. These worlds (and others we discover) often possess sets of conditions assumed to be completely hostile to life: as we know it. However, even life as we know it has shown us that it can really go off script sometimes. Whole new classes of extremophilic organisms have been discovered, and are still being uncovered in some really nasty corners of the world which show one thing: life’s ability to shuffle pieces around on the evolutionary chessboard has enabled it to live almost anywhere: in space, nuclear reactors, and the earth’s mantle. Bacteria have recently been discovered in Antarctica which literally use hydrogen as a food source! These organisms suggest that the traditional concept of a habitable zone: the right amount of heat, light and atmospheric pressure as we observe on earth need not necessarily apply to alien planets.

Tidally locked exoplanets

These are worlds which orbit their star(s) with one side permanently facing inward. The obvious ramifications of this: the side facing the star obviously has a much greater actinic flux than the planets night side. Translation: it is likely a scorched wasteland, where temperatures are oven-like. On the dark side we expect to find extremes of temperature at the opposite end of the scale. This side would be frozen and permanently dark. Overall, the planet doesn’t seem to hold much hope for life. It is believed that a good percentage of confirmed explanets are locked into tight orbits around their stars. Often these worlds take a few days (or less) to complete an orbit, and they are most likely tidally locked as a result. But all hope is not lost. The discovery of water ice in permanently shadowed craters on worlds as hostile as mercury and the moon leads many researchers to believe similar regions could exist on tidally locked exoplanets. Such water filled craters lie within the Terminator, the boundary between a planets day and night side. On a larger object such as an exoplanet, small strips of habitability could exist, situated in literally a permanent twilight zone. Twilight Zones of habitability could be a surprising spot for life to appear… In such a situation, the habitable zone as we define it would not be as dependant on distance from a star.

No Habitable Zone?

The recent discovery of two rogue planets lends itself to another interesting scenario. These rogue worlds are planets which aren’t gravitationally bound to a solar system. They are believed to be quite common. Current estimates have the complement of wandering worlds in the milky way galaxy at approximately two billion. How could such exotic locations possibly host life? Because geothermal or tidal heating could provide conditions in which life could possibly eke out a niche. Tidal heating is a mechanism for internal heating which has been observed in several frozen, distant worlds in our own solar system. Europa (mentioned above) and Enceladus likely possess subsurface oceans of liquid briny water. The heating for this comes from the gravitational stresses caused by interactions with nearby worlds. In the case of Europa and Enceladus their elliptical orbits around Jupiter and Saturn respectively cause an ebb and flow of tidal flexing in their rocky cores. Such frictional heating may even give rise to fissures and hydrothermal vents providing possible locales for biogenesis, as may have been the case here on earth. These frozen worlds appear lifeless, but appearances could be deceiving. Whilst far beyond the habitable zone of this solar system, the presence of life on either world would lead to further redefinition of habitable zones. Exoplanets are believed to number in the trillions in this galaxy and the recent discovery of the first known exomoon suggests that moons could be even more numerous. After all, in our solar system moons and natural satellites outnumber the planets by ten to one. Habitability on any of these worlds opens up the options for researchers observing distant solar systems for signs of life.

To the Weird..

Last but definitely not least. A benchmark of habitability as we define it for earth based life is that, overall, the environment should be fairly benign in order for life to have a chance. Earth itself only became habitable after billions of years of incredible geological upheaval and intense bombardment from outer space. Not only that, the presence of a thick atmosphere afforded protection from cosmic rays pumped out by a young sun. A class of exoplanets known as super earthsmay be able to support life despite often being in orbit around extremely energetic stars such as red dwarfs. These stars are tiny, often having only ten percent of the mass of our sun, but they are nasty. Frequently they have been seen producing extreme solar flare activity. This image shows a solar flare being generated by the red dwarf star DG Canum Vernaticorum (DG CVn). To put it in perspective the most powerful solar flare observed on our sun was rated X45 on a standard scale used to gauge glare events. In comparison DG CVn was rated X100,000: 10,000 times more powerful! At its peak the DG CVn flare reached temperatures 12 times hotter than the core of the sun! NASAs SWIFT observed this event over 11 days, recording the most powerful flare ever recorded. Image: NASA/SWIFT It stands to reason that any nearby planets would be baked into oblivion by the levels of energy being produced during such events. But larger rocky worlds such as super earths could provide a slim chance of life. Super earths are rocky worlds ranging in size from three to five times larger than Earth. Their mantle and outer layers could act as a shield against radiation, enabling any lifeforms present to carry on in subsurface biospheres, akin to recently discovered microbial biospheres deep in the earth’s crust. Lifeless surfaces could hide thriving ecosystems throughout the galaxy, or even beyond. Even neutron stars could harbour life bearing worlds if conditions are just right. These stellar objects don’t seem like an ideal location for life, but again a suitably large and dense world could provide safe harbour against lethal X-rays and other electromagnetic nastiness. Small worlds could be destroyed if they strayed too close, but if a super earth lay at a safe distance, who knows?

A Final Thought….

In this overview it’s been shown that life can theoretically exist outside the traditional confines imposed by earth based habitability criteria. However, I’ve only looked at planet based life… Who knows what else is out there? That’s a whole new type of thinking. Thanks for reading! I have a new video coming, which will be based upon this blog post. In the meantime, here are some speculations on a habitable moon in the distant past. P. S.. I have recently set up an online store, featuring my designs on a range of products, any of which would make fantastic and unique gifts! Take a look: https://www.redbubble.com/people/AstroBiological?asc=u All images © AstroAF Designs unless specified in image caption.
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#Astrobiology

Were I offered the chance to study again, I know what I would do. Astrobiology. In the last few years it’s been something I’ve followed. The trouble is, I’m easily interested in almost anything I come across. However, I would study astrobiology in a heartbeat.  So, what is astrobiology? 

Ever since humanity made its first baby steps beyond our thin layer of atmosohere astrobiology has looked to the stars, emerging as a discipline in its own right. It is the study of life on other worlds. Moreover, it is the study of life itself and asks the question: could life exist anywhere else? 

We’ve all seen the movies and heard stories. The idea of life on other worlds has had a vice like grip on the human imagination for a very long time. Every single culture on Earth has some accounts of visitors from the sky and encounters with otherworldly beings.

“Ezekiel’s Vision” by Mattheaus Merian. Image: Wikimedia Commons

From Judeo-Christian mythology and tradition to the various disparate and yet somewhat homogenous mythologies of Australia’s aboriginal people, it seems we’ve had visitors from the sky for quite some time.

Wandjina rock art, from the Kimberley Region of Western Australia. Image: Wikipedia

 At least so the stories go. Those stories will persist in one form or another for a long time to come, and the popular imagination is still fired up with tales of otherworldly visitors. Just trawl social media sometime and you’ll see what I mean. A search on YouTube: that paragon of level headedness, for a term such as “Area 51” will yield a miasma of conspiracy theories, alien “sightings” and general silly nonsense. Many of these videos have had millions of views. In my first search one particular video had over 20 million views. It was a “sighting” of an alien strolling across a road in some generic American desert setting. 

20 million views? Seriously?

People are eating this stuff up. But what does it have to do with astrobiology? Our desire for interstellar neighbours is always a little, shall we say, elitist? Does all extraterrestrial life need to be flying around in advanced spacecraft and spying on us: the cosmic equivalent of an ant farm? 

An early version of the Big Brother house. Image: Factzoo.com

(Are we that fascinating?)
Astrobiology specifically looks for life beyond earth. That life doesn’t need to be a wookie or a Borg drone. Something as simple as a bacterium would rock the worlds of astrobiologists everywhere. 

Missions to other worlds in the solar system have had this in mind for decades now. Missions to Mars almost turned the science world on its head when micro traces believed to be produced by single celled organisms were relayed back to space agencies. Big news indeed. Life on another world. Not Yoda, to be sure, but better! The jury is still out on this “evidence” but time will tell!

Possible biogenic structures, found in the Alan Halls meteorite, Antarctica in 1996. Image: NASA

You see, astrobiology is the search for life beyond earth. It is the application of a diverse set of scientific disciplines (which includes but isn’t restricted to) chemistry, geology, biology, planetolgy,  ecology and astronomy to look for anything. Any life at all. If human or robotic explorers ventured across the gulf of space and found something as simple as a bacterium it would be a massive deal. From the time of earth’s formation circa 4.6 billion years ago life took around a 

Life really was pushing it uphill in the beginning. Image: NASA/JPL

billion years to appear. The story of life isn’t the key point here. On earth life still took a long time to gain traction. It was only around 800 million years ago that anything as complex as a sponge first appeared, and it went through a pounding before all this happened. The Late Heavy Bombardment, a highly toxic and reducing atmosphere; likely similar to that on Titan today, which was replaced by another highly toxic atmosphere: oxygen. This change led to the greatest mass extinction this planet has ever known. An irradiated, toxic lethal planet somehow gave rise to life. 
Astrobiology looks at life on this primeval earth and posits the question: if it could make it here, it kind of stands to reason that it could develop somewhere else. Earth now is a benign paradise, possessing a very particular set of attributes that enable life to thrive. Among these; a thick atmosphere and life giving heat from a nearby sun which respectively enable liquid water to exist at the surface and provide the fundamental energy for life to prosper. Earth possesses an active magnetosphere which shields life from cosmic radiation.  These are only some of the factors that make earth just right, like the proverbial bowl of porridge. In fact, in honour of that famous metaphor, Earth is said to orbit the Sun in a “Goldilocks Zone” This means that we are just far enough from the sun that the temperature range is just right for liquid water to exist at its surface. Hence the thing with the porridge.

Many other worlds we’ve examined don’t have any or all of these qualities, but that’s no reason to dismiss them. 

Life is seemingly turning up everywhere we look these days, and the more we look the more we see that life is extremely tenacious    From the clouds above us to hadean environments deep within the earth’s crust to active nuclear reactors life seems to be able to survive anywhere. 


That’s what gives astrobiologists hope.
This post is to be the outline of an upcoming episode on my “Ben’s Lab” YouTube channel. For any who are following the channel (thank you!) It will be undergoing renovations. The subject matter will focus more on things near and dear to my heart, and astrobiology is one of those things!  If you like astrobiology please leave suggestions for episode ideas in the comments, or share this with others who like it as well.

References and resources:
This list is not comprehensive and is intended to begin those who are interested on beginning their own research; 

https://astrobiology.nasa.gov/about/
https://en.m.wikipedia.org/wiki/Allan_Hills_84001
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1932751/
https://www.scientificamerican.com/article/life-found-deep-inside-earths-oceanic-crust/
https://en.m.wikipedia.org/wiki/Deinococcus_radiodurans

#SignalDegradation

Soundtrack: the opening theme of “The Big Bang Theory”

 

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When I was in university I majored in Earth Sciences and Biology, thinking this was some sort of suitable compromise with my then academic ambitions. You see, I’d really wanted to study palaeontology. It had been one of those vague childhood longings that had not quite managed to be squeezed into a torpor by life. Having these two majors seemed to make sense. For part of the day I was studying geology, geophysics and sedimentary processes.  For the remainder I was buried in lower eukaryotes,  molecular and microbiology and animal physiology. Dinosaurs are somewhere in the midst of all that, right?

Kind of. Well the dinosaurs fell by the wayside (became extinct?) and I found myself really liking pretty much everything else I was studying. Learning is a joy in itself. Whilst in university I was privileged to attend lectures given by Dr Leigh Burgoyne. For those unfamiliar with molecular biology Dr Burgoyne is half of a pair of scientists who elucidated the structure of chromatin.

What tha’ heck is chromatin? Chromatin is a complex of structural proteins that enable Deoxyribose nucleic acid (DNA) to play the ultimate game of Tetris. DNA is a very wily molecule, which I’ve touched on in a previous post. It has insane data storage potential, and a single strand of DNA is three metres long! Now you understand why it needs some mad packaging skills to squeeze into something the size of one of your cells. That’s basically what chromatin does.

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Life wouldn’t work if it didn’t have an epic case of OCD.

 

I remember a single lecture given by Dr Burgoyne. To be honest, I remember very little of about nine-tenths of it (it’s still stashed in my head somewhere), but then it seemed like he really began speaking.

He told us the tale of life….

In order to parse what he told us I need to paraphrase what he said. I need to mix metaphors and go off on tangents.

Now, any students of science out there will have butted heads with statistics and probability whilst studying. I’m not in any way being elitist here. Most sane people know that the universe is a collection of freakish accidents all cycling constantly and spewing out more freakish accidents. Somehow, a stream of such accidents has led to you. As Terry Pratchett said in one of his Discworld novels;

Million to one chances happen nine times out of ten.”

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We are all freak accidents. Every single person- every single thing– alive today is a current iteration of a single freak accident that took place in a warm, shallow pond nearly 4 billion years ago. Or trapped inside ice. Or on the slope of a deep-sea hydrothermal vent. On a sheet of clay even.

Hell, maybe it was on the shifting gravel filled terrain of a passing comet. Who knows? I’m sure not going to be presumptuous. Theories on the origin of life abound. I strongly suggest venturing out into the literature and checking these out for yourself.

Freak accident.

That accident somehow decided it wanted to keep on keeping on. So it went looking for other freak accidents to consume. This in itself required some changes. And so it began.

Life.

Life is not just a thing in itself.  Life is all of the things that life does. Emergence gave us life.

Life got hungry. Life went looking. Life grew. At some point life joined forces with other life, going onto business. These partnerships have lasted till this day. Life became stronger, faster. Like human explorers expanding forever westwards life travelled. It began to see. It began to conquer. The entire planet was a vast new frontier. A planet of accidents and danger. At every single turn life met with struggle, and it was forced to sink or swim.

So it either sank or swam. You’re only here right now, sitting on this train, or hiding in the toilet for a few minutes because every single one of your ancestors swam. If the theory of a multiverse holds any water, then in another universe it’s someone else reading here in this spot. Or I never existed to write this and you’re watching a Minecraft walk through on YouTube instead. Whatever floats your boat.

I remember the lecture. Dr Burgoyne gave his thoughts on the astronomical run of good luck that led to everyone being in that lecture theatre. I swear, you could have heard a pin drop. People were listening. It was an amazing moment.

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NOT the lecture in question, but you get the picture..

What’s more amazing than the fact that we are here at all? The fact that in nearly four billion years of life, the central message of life has only degraded by a few percent! That’s just nuts! Think about it!

DNA (sometimes RNA) is the information storage molecule for all life. RNA stores the genetic information within viruses, which inhabit a shadowy world somewhere between the living and the abiotic world. For the sake of simplicity I will refer only to DNA.  We’re all scientifical enough to not get all Sheldon Cooper when I hold up DNA  as THE information storage molecule.

Moving on Ben.

Think of life as a signal, and DNA is the filter, tuning out cosmic background clutter and refining it into something pretty improbable. Like you. At a point in time the signal was set in motion. Whether it was in a pond, an iceberg or a comet, life got going; using some kind of information storage in order to send copies of itself out into the big bad world.

That signal’s been around for a very long time, replicating and transcribing and reinventing itself in an endless profusion of forms. Some very ancient cellular machinery has been hard at work, replicating DNA with incredible fidelity. What amazes me about all of this is that cellular automata (proteins for the most part) carry out this herculean task. Proteins aren’t alive. They are essential players in the mechanics of life, but they aren’t alive in themselves. Some proteins are capable of replication, but that’s another post in itself (and an interesting one too).

Let’s play the Pepsi taste challenge, but instead of cola drinks let’s compare say…YOU and a bacterium. That seems a bit silly, right? There couldn’t possibly be two more different organisms on the face of the planet. Let’s put aside the fact that your particular body is about ninety percent bacteria in terms of numbers. Let’s focus on the ten percent of you that’s actually YOU. Ok. You have eyes, ears and wear pants. You’re reading this post on a phone, computer or tablet.

Keyword: Reading.

Implication: highly complex brain along with associated neuronal infrastructure, from which emerges this nebulous thing called a consciousness. You can’t point at it, but you know it’s there.

You wear clothes. I wear warm clothes right now, because it’s a cold day. You’re probably drinking or eating something right now. I’m sucking down a coffee. Implications of this: you have a digestive system, along with associated waste disposal mechanisms. You have fingers, and nostrils to stick them up sometimes, leading to lungs. You can drive a car. Other creatures like you have walked on the Moon and made brainless YouTube videos.

Bacteria, by comparison to you, are a little simplistic right?

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E. coli. Doesn’t seem too impressive, right?

Hah!

Time to shatter some illusions. You may have heard that human beings and chimpanzees are 98 percent genetically identical. Only 2 percent of your DNA makes you human, compared to a chimp. Well, brace yourself.

You and that bacterium you look down upon so loftily differ genetically by 10 percent. TEN percent! In nearly four billion years, bacteria, one of the oldest lineages of life to exist, have barely changed. All of those changes have been tiny and incremental, giving rise to the kaleidoscopic variety of life that runs, flies and swims across this planet now. That’s pretty amazing. Just knowing something like that feels like being privy to some cosmic secret. Hell, I think it is.

bacteria
Ha! Thought you were hot stuff, didn’t you?

Let’s keep going with this biological Pepsi taste challenge.

Can you keep gossip to yourself? We live in an age where information and reality are becoming blurred. The very existence of Alt-news, Alt-facts, false news, filter bubbles and a host of other ills plaguing the last few bastions of enlightenment are nothing new. Have you ever played the game of Chinese whispers? I’m Australian, so it may be called something different where you come from. A story is spoken, or whispered into the ear of a player, who whispers it into the ear of the next, and so on. It’s fun to see how the story spontaneously mutates, changing as it goes. Sometimes it reaches the final person in the line a completely new beast. This string of mutations happens quickly, completely changing the original story, and all in a few moments.

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Social media. It has a weapons grade case of Chinese whispers….

Think of your genetic information, or genome, as a book. Blindly and efficiently this book is replicated. The two entwined threads in it’s double helix are unwound by DNA helicase. Then DNA polymerase attaches to the strands, and attaches complementary nucleotides to their respective exposed base pairs along the strand. This is an extremely cut down version of what happens, but all you really need to know in the context of this post is this: it all happens extremely quickly. In the bacterium Eschericia coli, replication can speed along at the rate of around 1,000 nucleotides per second. DNA polymerase in your cells works much more slowly, at a snail-like 50 nucleotides per second. Such speeds are achieved by many polymerases attaching to unfettered DNA strands. Many hands make light work after all. How much can you achieve in one second? All of this goes to show that parallel processing is one of Nature’s oldest tricks.

You’d be completely reasonable to assume that such a process would be fraught with errors. It is. But unlike the game of Chinese whispers, or the rant on Facebook, errors of interpretation and transcription happen much more infrequently. After all, if DNA replication was untidy and prone to errors life would have eventually never taken off. Early in the piece evolution made sure that efficient replication of information was critical. Some mutation is good, but too much is bad. A few mutations here and there over the eons have given rise to you. Too much mutation and life breaks down. So what constitutes a few mutations here and there?

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Without organisation and proofreading, life would maybe have made it this far….

For every 10 billion base pairs that are replicated, approximately 1 error gets through. DNA polymerase on its own is pretty good at what it does. Being completely automatic it doesn’t have a pesky brain doing bothersome things like over thinking or day-dreaming. It isn’t perfect, however. Left to itself, DNA polymerase will stuff things up to the order of 1 bad base pair in every 100 million replicated. A suite of repair enzymes are at its disposal, tidying up these mistakes and getting replication fidelity up to the 1 in 10 billion mark.

Boy, talk about an amateur. Me, that is. I’m a chef by profession. After 22 years of sweating it out in kitchens, I still manage to burn at least one piece of bread a day (don’t tell anyone). If pieces of toast were living things, then at my hands not only would they never evolve, they would become extinct long before they ever had a chance. Maybe they should have enzymes working in kitchens.

Maybe not.

So, I hope you see what I mean. Every single living thing on earth (and who knows where else) exists purely because extremely high fidelity of replication has evolved to ensure against excessive mutation. Another way of putting it is; even after four billion years of nearby supernovae, disasters, extinctions, geochemical catastrophes and endless strife, life has been able to hold on, and all because of extremely faithful data storage and propagation. If we ourselves can evolve past our own tendency to conflate every thing we hear and describe, maybe we could stick around for a while longer too.

Life is a signal, a signal that can’t be broken. Let’s learn from it.

 

Ben.

Who writes the #Writer?

If you’re a fan of the fantastic and the (almost) magical, then you’ll know that it’s getting harder and harder to get through a single day without being almost paralysed by the veritable flood of big announcements being unleashed upon the world. 
Gravity waves, TRAPPIST-1, Juno and it’s watchful eye on Jupiter. All just more science candy to rot our teeth with. 

I LOVE IT!

But here’s a little secret. 

There’s no magic like old magic. Warning label: this post will contain references to talking lions and impossible cosmologies. 

The universe and all within is an impossible cornucopia of wonder. J.R.R. Tolkien once spoke of the wonders of the unexplored vista in fiction. The universe is still (and always will be) an unexplored vista, like some dark brooding mountain range; its fell winds filling a lost band of travellers with foreboding. The mountain ranges are the same in every fantasy novel I ever read: cruel, dark and vast. I would join the travellers on their journey; be they the Fellowship of the Ring, Atreyu and companions finding a way through the Nothing or the Pevensey children, seeking Aslan. I would see the same mountains or vistas they would see and wonder what was in them, watching the story unfold. 

Did you ever wonder what was beyond  those mountains?  Nameless lands and other unrecorded epic histories and struggles? Life? Death? Infinity? Cyborg armadillos? A back door out into some rat infested alley somewhere? I spent a lot of time beyond the borders of these imaginary lands, seeing them as some kind of dreamlike state attached by imaginary geography to the main tale. Like junk DNA they didn’t seem to play any kind of part in the story, yet they also provided it with further structure. Playing a very important role by simply hanging there, forever out of reach. 

In a sense the distant past is like this imaginary land, especially the very distant past and in particular those very very first moments. Maybe even the time before time. How far back can we go really? Like the resurrection of Aslan in “The Lion, the Witch and the Wardrobe, in which the Lord of Narnia drew power from a time before time, is everything built on something else? 

Life is such a thing.

Contemporary scientific dogma explains life as a phenomenon emerging from inanimate disorder. To the scientific mind this makes intuitive sense: a bit of stuff and another bit of stuff merged or were bonded chemically and some miraculous act of transmutation took place. Life appeared: self replicating systems, handing down and reliant upon the seamless transmission of information/instructions. Hiccups in this basic routine were bound to happen of course. If biological information transmission were completely flawless I wouldn’t be sitting here in a McDonald’s writing this, I’d still be a blob of stuff flopping around in some warm little pond somewhere. Obviously I’ve used the simplest description possible. Life changes in response to environmental changes and pressures, but I’m not going  to have a blog post blowout by hyperlinking into a discussion about evolution. 

Where was I? Life. 

 I’m thinking now about this process of emergence.  Life itself is (at the very least) an emergent property, arising somewhere from within the girders and tangled architecture of Nature. Is it created by this chemical and physical architecture, or was the promise of life already hiding in the basement somewhere?

A snapshot of the cosmic microwave background radiation. The ultimate family snapshot: everyone’s in it!

This emergence is a built in property of the universe. Quantum theory holds that our perception of the universe calls it into existence. If this is true, then what of a time before life or perception even existed? Did the universe even exist before we came along? “We” being life that is. We of course aren’t the first things to experience the universe. Even a jellyfish experiences existence in it’s own way. I must make here a distinction between perception and intelligent perception. 
Obviously the universe existed before us. Take whatever side of the fence you like: religion or science. We can all explain the universe and we are all intrinsically aware that the universe was created and was here long before the first living thing flopped out of the primordial mud. 

This emergence of life was always meant to happen. The universe cycles itself, refreshing every second, every single passing of whatever fundamental subunit of time ticks by. We perceive it into existence, but it was perceived by things before us, things before them and so on.  But what of the first thing? What perceived the universe before anything even knew it was there?

The universe has always contained the framework for perception. Patterns in inanimate nature repeat themselves in biology.  

When I was at university I gave some thought to the emergence of multicellular life. After completing my degree I kept studying, doing an Honours year. I originally wanted to study biofilms. Of course the project mutated and became unrecognisable. My supervisor steered me towards something completely different, but I always thought about the emergence of something fundamentally different to single celled life. I felt that simplistic biological structures like biofilms represented a step in the transition from single celled existence to colonial organisms and from there to multicellularity. 

Take a wild guess what got me thinking about multi celled organisms emerging like this; ready made as it were.

Coffee. 

I was in one of the University cafés,  up on the hill behind the sciences building. As did many others I spent a lot of time here studying, reading or just thinking. It was quiet and I had actually been thinking about multicellularity on this day when I looked down at my coffee. I have a tendency to forget things when I’m pondering the world and my coffee had gone cold. 

The wrinkly skin that had formed on top got me thinking. I remember drawing it, doodling it on a corner of a notebook page, recognising something.  It looked exactly like all kinds of biological structures, in particular biological infrastructure such as a circulatory network. The branching structure or pattern we see here is so familiar to us we don’t even think about it.

And so it began. I got thinking..

We see so many repeating patterns and structures in the natural world that they are almost white noise. The forking of tree branches or blood vessels, the winding of streams and rivers and the somehow disciplined swirling of clouds are very familiar to us all. It’s interesting how the same kinds of patterns appear both spontaneously, as in the case of rivers, or under the guidance of carefully meted out biological information (tree branches etc).

Physarum polycephalum, a bizarre and fascinating oddity.

*Update 27/07/2017

This video summarised some of the points of this post really well.  Enjoy the heck out of it. Via Biographic. 


Consider this image. 

A river winds through a muddy delta plain, stretching toward the brackish waters of an estuary. 

Now consider this one:

A stagnant shallow pond, at Mutton Cove Conservation Reserve, Port Adelaide.

The branching pattern running through the midst of this mat is quite reminiscent of a river system. In fact, you’ve most likely figured out that these are both the same image. This is why I’ve used this image. It represents a key point I’m trying to make. 

The mat is likely mostly microbial, or composed of biological material: microorganisms,  waste products, in  addition to inorganic muds or silt. The branching  and bifurcations within the mud are most likely formed due to abiotic factors, in the same way that synaerisis cracks form in muddy lake bottoms as the last of their water dries.

My question: could such structures;  formed by innocuous natural processes, provide templates for biological processes? Biofilms are known to possess channels and a certain level of internal structure.  Some of these structures are similar both in form and function to structures that perform analogous tasks in multicellular organisms.

Did early multicellular life get an organisational leg up from a deeply mathematical universe, in which all manner of patterns appear in a multitude of environments?

I say the universe is deeply mathematical, but I will admit here and now I am no mathematician. It’s just always seemed apparent that the universe operates around a very secretive and mysterious set of guidelines. In the same way that a businessman from Sydney can walk into a McDonald’s in New Delhi and expect exactly the same Big Mac he’d get in Moscow, so it follows that rivers of liquid hydrocarbons on Titan form branching channels and patterns; following the same recipe as rivers of water on Earth.
What I mean is that some things just never change, wherever you may be in the local Universe. If you were standing on an exoplanet passably similar to Earth you’d see flows and channels just like those on Earth. One of the planets orbiting TRAPPIST-1 may make a good setting for this imaginary walk. The sky is dark. It’s like a permanent sunset: a red hue washes over a rocky landscape. You’re standing on a low cliff, looking down at a river. It looks like any river on earth. OR, just like the river systems on Titan.

River channels on Titan, carved and eroded by liquid hydrocarbons. Image: NASA/JPL

This similarity is spontaneous. That’s something we all intuitively know. This is what I’m getting at. If life formed spontaneously as a result of natural laws, then life- and more complex life would arise on other worlds.  Depending on its environments and circumstances it will obviously be different to life on earth, but there will also be similarities. 
It’s all about infrastructure. Infrastructure arises unbidden in all manner of systems. 

A flock of starlings is a system.

Spaghetti on toast is not.

A system is a collective of interconnected parts or processes, all acting within the context of a greater whole. A flock of starlings differs from spaghetti on toast in this fundamental aspect. The flock appears chaotic, but in fact behaves according to rules which are seemingly set in stone.  The spaghetti shows no flavour of interconnectedness nor any kind of behaviour. The strands do not interact and so are unable to work together to prevent being eaten by me. The flock of starlings however can.  

I’ll take the spaghetti. 

The swarming behaviour exhibited by the birds and other creatures which swarm (locusts, Monarch butterflies etc) is an emergent property, arising from the interactions between sub units. 

Back to infrastructure. The flock of starlings acts as it does because all of the birds can see each other or otherwise interact with each other in some way. Mechanisms exist by which the birds connect to each other, and so something new emerges from a seemingly disparate collection of birds. Consider a city.  Many cities began as gatherings of family groups or tribes. For these small groups such an existence worked. Not much infrastructure other than language, common customs and some simple rules were needed in order for these simple societies to function. 

But then the families began to grow. Other villages were discovered. Tribes went to war. Other villages and tribes were conquered. Populations and customs began to change as other cultures and ideas sped up progress.  Farming was discovered: trade followed. Technology developed. This is all part of the growth of a society,  and it is an analogue for the evolution of multicellular life. As time goes on infrastructure is a necessity. Roads, money, writing, advanced modes of travel, all develop as a natural by product of the growth of a society. A city becomes an organic thing. It sprawls across a landscape, complete with a venous network of roads and railways. Communications dart back and forth along phone lines and fibre optic lines: the equivalent of nerves, enabling disparate sections of the city to be aware of outside forces and distant events. From a distance these branching roads and lines could bear a passing resemblance to biological infrastructure. Even lower eukaryotes appear to understand this:

This is the famous example of a slime mold set to work redesigning Tokyo’s rail network! Many experiment have shown these unbelievable organisms effortlessly redesigning Spanish and Portuguese rail networks: often rendering them more efficient than the human engineers!

So at a glance at least it looks as though the collective behaviour shown by a slime mold runs along similar lines to the growth of a city. Lines of infrastructure, connecting sub units, create a gestalt entity; something more than the sum of its parts. 

If life (and in particular multicellular life) arose due to a proclivity for exploiting the connective properties of certain naturally recurring patterns and structures, how did life figure this out? Obviously roads didn’t appear before cities. But in every single city on earth roads could be found. The idea of a road always existed. Roads were inevitable.

Off on a wild tangent? Is this a flight of fancy? Maybe, maybe not.  What do you think? Self organisation and emergence aren’t just products of group behaviour. They are inherent tendencies, built into the fabric of space and time. Feel free to pipe in with your opinion. Thanks for reading. It’s been a long post, and possibly rambling, but it’s a blog.  Not the six o’clock news.

Cheers,

Ben.

P.S.

Check out Biographic on YouTube and Twitter. Well worth it.

Take a look at bioGraphic (@bioGraphic): https://twitter.com/bioGraphic?s=09

In the shadow of #Dinosaurs

Some readers may remember a recent post about people and their relationship with science. In particular I ran a poll on Twitter,  asking about “gateway drugs”. What got people initially fired up about about science? A small cross section of followers responded:

For insights into these “gateway drugs” check out this post

This post will take us on a joyful (and maybe self indulgent) look at my own gateway drug: dinosaurs. A very recent visit to the Melbourne Museum had me making a bee line for the dinosaur and fossil exhibits. Even now, in my forties these fascinating relics of the bygone age to top all bygone ages have a powerful hold over me. 

Part of this hold is their ability to grip our imaginations. “Jurassic Park” was for me a life changing event. I still recall the hushed awe I felt when I saw that Brachiosaurus for the first time. Up until then I had only imagined myself walking the steppes and plains of Mesozoic earth; either walking alongside these creatures or watching them fight, struggle, roar and sink into mud. I was with the dinosaurs in a very real sense. When I read books about them or saw pictures of them it was like I was there…

“It’s a warm afternoon, somewhere in mid Cretaceous Queensland, Australia. A small group of hadrosaurids are approaching a shallow river with caution. For miles in all directions a tangled patchwork of marshland and conifer forest is home to communities of dinosaurs who have made this delta their home for countless generations. This is a group of Muttaburrasaurus,  and they bleat and honk quietly,  instinctively hushed. 

An iconic Australian dinosaur.

Small waves lap at their feet as they wade out into the river and begin drinking. The Sun has a sharp edge to it and the creatures are lapping noisily, drinking their fill. Clouds of flies harass them.
The group has been cautious around this waterway lately for a reason. 

By the time the group is fleeing the water, braying loudly in a tone of animal panic it’s too late for one of them. A younger individual is flailing, now kicking weakly in the water and sending shock waves up and downstream that will bring curious scavengers like sharks along. As the juvenile dinosaur is pulled beneath the water it sees another member of it’s herd;  watching from the bank of the river. 

A kronosaurus has taken of late to patrolling the river, recognising the easy pickings to be had. Herds of dinosaurs like these muttaburrasaurus are an irresistable draw. It’s latest victim is dead in less than three minutes; as it’s blood supply gushes away, mingling with the river…

STOP READING!

 See? It’s like a perfect fantasy world. Perfect because it actually existed!

The Dinosaur walk exhibit at the Melbourne Museum allows one to feel this wonder again.

A pair of carnivores greet you at the entrance to the museum’s fossil exhibits

It’s school holidays as I write here in Australia. The skeletons are surrounded by throngs of kids (and equally excited parents I would dare say). Could there be some budding scientists in that mix somewhere? Maybe one day a future palaeontologist or biologist will recall this day, remembering how the Tarbosaurus skeleton loomed large, glowering down at them. They might recall a mixture of excitement and wonder that will stay with them their whole lives.

An adolescent Tarbosaurus, smaller cousin to the infamous Tyrranosaurus Rex.

I’m surrounded by screens. Phones are out, tablets are pointed at the displays and the museum has touchscreens everywhere, where kids are jostling to interact with the information being presented on them. 

As seems to be a standard thing these days the children are focusing more on this electronica. I note this and tell myself what my younger self would have seen when looking up at these giants….

A cool wind slides across a vast expanse of sandy bushland, somewhere in what will one day be Mongolia. The time: not really important to the young Tarbosaurus creeping along a dried river bed,  eyeing new prey. For the human observers, borne by imagination into this distant past let’s call it approximately 68 million years before palaeontology is even invented.

Food is a little scarce out here for the tyrannosaurid.  Larger Tarbosaurs in the region have staked their claims, carving out large tracts of territory. The young dinosaur isn’t starving though. It has discovered these small herds of sheep sized creatures; protoceratops. These are, as their name suggests, ancestors to the tank-like horned dinosaurs of the late Cretaceous: Triceratops,  Styraccosaurus and the like.  The diminutive reptiles are abundant here, staying in groups where there is safety in numbers. They’re savage little fighters too. Seeping wounds on the Tarbosaur’s lower legs and belly give testament to this. They have discovered strength in numbers.

Until they need to lay their eggs. Using the slope of a shallow dune as cover the Tarbosaurus is following the strong scent of a lone female. She’s busy laying her eggs in a neat ring around the edge of a shallow depression she’s dug. She is too focused on her labours, and is unable to defend herself as a giant three toed foot crushes several eggs and powerful jaws lock around her neck. Dagger like teeth finish her quickly, before she can even bleat in pain…

It all happened so fast..

Who knows what has brought these bones all the way across the world to this museum? The lives of these creatures is impossible not to wonder about as I find more skeletons.

Not all dinosaurs here hail from overseas. Australian dinosaurs take pride of place. 

Qantassaurus intrepidus was a small bipedal hypsilophodontid which hailed from what is now-again- modern day Queensland. Along with Dinosaur Cove in Victoria Queensland is becoming a veritable hot bed of fossil discoveries. Qantassaurus is interesting in the context of this exhibit because it’s appearance has been almost entirely reconstructed from fragmentary fossilised teeth.

This alone speaks volumes of the importance of imagination to a scientist, and to the detective work they perform as a matter of their work…

It’s morning in Jurassic Queensland. A pair of rabbit sized mammals are squealing noisily, squabbling over the remains of a dog sized reptile . There isn’t much left. Other scavengers have long since picked the carcass to pieces. The combatants snarl and wrestle over a tooth, desperate to claim any prize in this battle. A victor emerges, and the loser scuttles off into surrounding undergrowth,  eager to not become prey itself….

 A few teeth! From a few teeth (and several educated guesses) palaeontologists are able to glean information: the animal’s lifestyle, diet, and size.

Walking around the exhibit, visitors find themselves hopping backward and forward through time…

Australia, one million years ago, sometime during the Pleistocene Period. Vast red emptiness spans the continental interior. This is a dry, desert continent and life here is tough. A lone predator stalks the deserts and arid grasslands, preying on the megafauna that has evolved here in isolation from the rest of the world. 

A lizard, looking something like a seven metre long Komodo Dragon stalks the scrappy salt bush that stretches as far as the eye can in all directions. Some day a new predator will arrive here; a bizarre two legged beast that will conquer these lands and seize their place at the top of the food chain. 

Top of the pile until new competition arrived, Megalania was a true apex predator, stalking Pleistocene Australia.

For now, the harsh sun blisters the land but Megalania hides in shadows, eyeing it’s next victim…A pair of Diprotodon grazes on some nearby bushes. They are too intent on their meal. These giant marsupials are the ancient Australian equivalent of the rhinoceros,  filling the same ecological niche.

Diprotodon, along with all other Australian megafauna died out circa 46000 years ago; a victim of climate change and human predation.

The Diprotodon aren’t fast movers at the best of times, relying mainly on their size as a means of warding off predators. The youngster, however, is brought down quickly as the ancient reptile dashes out with a freakish burst of speed. The mother is equipped with a fearsome pair of incisors. Normally she uses it to extract roots and vegetation from the dry red soil

Megalania is rewarded with a broken foot as it is trampled by an enraged mother weighing several tonnes. Those teeth inflict a bloody toll as well,  and the defeated predator is forced to retreat,  slinking quickly back into the scrub….

Honestly, having just come back from a trip to outback Australia, surrounded by some of the oldest mountains in the world 

For 380 million years the vast slab like Grampians have dominated the Victorian landscape.

I can almost smell these long lost landscapes. I can stand on the cusp of a red dune, watching whirly-whirlies (dust devils) skipping across the endlessness of an inland sand sea. Where I stand in this dream scape was once the floor of an ocean: the Eromanga Sea. Imagine looking up from this spot, protected by the vast lengths of time between yourself and seeing elasmosaurs; graceful long necked giants gliding through the waters.
There are more posts to come on the very ancient world, and Australia in particular. I would love to hear other people’s dinosaur tales. I don’t think a half baked youtube video can do justice to these prehistoric beasts and their memory as much as the written word. Anyone can feel free to offer suggestions or their own experience growing up in the imaginary shadow of dinosaurs and the prehistoric world.


Unthinking Coordination in “Simple” Lifeforms

It’s another picture perfect day here in Adelaide,  South Australia. Despite the fact that Autumn has been with us a few weeks now I’m getting uncomfortably hot. I’m lying on my stomach on a small marina, my face hanging over the edge and inches from the water.

As is the (annoying) habit of our cat I’ve simply dropped down and parked myself right in the walkway. Why?

Jellyfish. Lots of them.

Getting out and looking for little beasties to photograph is a passion of mine. If I’ve managed to randomly bump into some caterpillar or spider I’ve never seen before,  then I pretty much have to clear my diary. I am not a professional photographer by any stretch, but it’s getting out there and seeing these things that’s important. Whilst walking along the wharves in Port Adelaide the sight of thousands upon thousands of jellyfish in the water has me reaching for my cameras, which are always in my car.

This swarm seems extremely out of place. I’ve already done a live stream on Periscope showing the good folks of Internet land this odd phenomenon, and now it’s time to really try and do it some justice.

A Jelly Family Tree

First off, these graceful creatures are Moon Jellies. They are extremely common in Australian waters. I have observed them now in the Port River in St Vincent’s Gulf, South Australia and in Darling Harbour, Sydney, New South Wales.  Moon jellies are a favourite food for many turtle species. Being easy to both eat and catch I could understand why. I was actually asked this very question during  my live stream.  One thing that heartens me during these live streams (and that I notice while watching others) is that people really like animals. In fact, wildlife seems to bring people together in a very positive way.

There’s some kind of take home message in this, don’t you think?

Moon Jelly is the common name for Aurelia aurita,  a species found globally. Jellyfish, along with sea pens, corals, anemones and hydra belong to the animal phylum Cnidaria. Approximately 10000 animal species belong in this group, and all are exclusively aquatic. Cnidaria are an extremely ancient group, with jellyfish fossils up to 500 million years old being discovered. Fossils believed to represent the Cnidarian crown group predate the Cambrian by around 200 million years. Cnidarians represent the oldest multi-organ animals known.

This fossilised jellyfish, found in Cambrian strata in Utah, is diagnostic of modern jellyfish spp. Image: PLOSone. 

The moon jellies, like all scyphozoans;  or true jellyfish, posess cnidocytes. These are specialised barb like cells which on coming into contact with prey (or anything for that matter) penetrate and inject venom into the recipient.

Micrograph of cnidocytes. Image: microscopy-uk.org.uk

These particular jellies are almost harmless to humans. In fact, it’s said that the only way to feel a sting from a moon jelly is to kiss one.

Not enticing.

Australia is however home to several species of jellyfish which are far more dangerous. We do posess our share of dangerous animals. Some of the most lethal venom on Earth can be found in Australian waters. From the tiny Irukandji jellyfish;

Big things come in small packages. The Irukandji jellyfish delivers one of the most lethal venoms on the planet.

To the Box jellyfish:

Just when you thought it was safe….cue menacing music..

The moon jellies gathered here in the Port River are weak swimmers at best and so are often found collected in estuaries and inlets in this way, caught by the tide. Observing these jellies showed them seemingly moving as one: the group seemed to surge in one direction, oscillating back and forth in a manner reminiscent of group behaviours: much as flocks of birds appear to move about as one. Empirical observation would seem to bolster this. The bell structure of most jellies seemed to point in the direction movement.

This is interesting. Jellyfish, along with other cnidarians, appear to have no (or at least very rudimentary) brains. They clearly have nothing we would recognise as a brain. Instead, their bodies are essentially a loosely interwoven collection of simple nerve networks, reacting and interacting with each other for the purposes of responding to stimuli.

This decentralisation of “administrative duties”, or biological anarchy is seen in some rather more advanced creatures. Octopuses are one example. It is now well known that octopuses are extremely intelligent, but these amazing animals are now thought to sit somewhere outside the traditional brain/body divide we have accepted as a basic paradigm of our own physiology.  Not only do octopuses have a brain, but their tentacles operate independently, acting with their own intelligence. Essentially the entire body of an octopus is it’s brain. Is this a feature of marine organisms and the result of marine existence?

While jellyfish could hardly be called intelligent, are we not giving them enough credit? Does living in an environment as featureless and homogenous as the ocean necessitate a particular brand of spatial intelligence and information processing?

Imagine a line representing a scale. This scale is that of intelligence: in particular the gradation from true brainlessness and pure instinct displayed by, say, bacteria to “higher” intelligence in which all memory, learning and response is coordinated by a complex central nervous system ( a brain. Think “human”).

On this line an octopus seems to sit somewhere beyond halfway. Able to perform complex tasks, and armed with a unique “whole body” intelligence the octopus is gaining a whole new respect.

The jellyfish appears to act wholly on pure instinct and autonomic response. I observe a swarm blindly clustering in a protected estuary and wonder. Decentralised nervous systems enable a different flavour of response to external stimuli. It speaks of a wholly different pathway by which intelligence could rise in the ocean. Terrestrial and marine environments could not be any more antithesis to each other. Land changes much more and over shorter periods of time than the sea. The land is a much harsher place in many ways. Organisms living on land have been forced over evolutionary time to undergo many more changes in order to survive: hard eggs, legs, and a much greater reliance on eyesight to name a few. Life in the ocean is vastly more stable. Does the existence of organisms such as horseshoe crabs, jellyfish, sponges and sharks, which have remained virtually unchanged for hundreds of millions of years give testament to this stability?

Where could a creature such as the jellyfish go, given time? The octopus, a simple mollusc, is an impressive example of a non human and quite alien intelligence. Do other forms of awareness and behaviour (that shown by jellyfish) constitute some new paradigm we haven’t recognised yet, and from which intelligence may someday emerge?