Category Archives: nature

Thirty Nine Light Years: Part Three

More transmissions come in from the TRAPPIST-1 system. Three worlds stand out from this family of seven rocky worlds, all huddled around a dim little red dwarf star.

There’s water here. Lots of it. Spectroscopic analysis first spotted it decades ago, but recent arrivals to the system are diving into new frontiers.

Back in our neck of the woods we’ve sent various missions beneath the ice. There’s a lot of ice covering a lot of water. Commercial operations have popped up all over the system using all of this water to make fuel. Europa Clippertook the first real good look at this little moon. Several fly throughs of Europan geysers showed clues the moon may harbour life.

TRAPPIST 1e has a single frozen ice cap, perched over the planet’s southern pole. The above image was taken by an underwater drone: one of dozens dispatched across the planet’s two small oceans. This expanse of ice is tiny, comparing in area to the north pole on Mars, but it’s rich with organics.

How rich?

A native moved across the drones field of view, investigating for a few moments and then darting back into the darkness. Attempting to locate the creature led the drone down into further unexplored depths.

A single close up image has been beamed back, digitised and speeding across 39 light years to astrobiologists on Earth. Not even Europa has yielded anything this concrete yet.

The presence of what appears to be a single eye denotes a certain level of biological sophistication. This denotes a long lineage of life on this distant world. TRAPPIST-1, like many other red dwarf stars is far older than our own sun, at between eight and ten billion years. This lifeform may have had a long time to evolve. Indeed, life may have appeared and disappeared more than once on this world, given such time frames.

The planet’s land (about sixty percent of it’s surface) is blanketed by vast regions of photosynthetic organisms which appear to use a pigment similar to retinal to pump oxygen into the atmosphere. This aerial view shows a plain of red grass-like organisms at the shore of a shallow inland lake.

Primitive photosynthetic life covers much of the planet, producing an oxygen rich atmosphere.

A thin veil of dust embraces the planet, forming a wispy but noticeable ring system. This material has already been detected spectroscopically, and researchers have been able to surmise some important data. TRAPPIST-1e was once an ocean world. Tentative detection of carbon, oxygen and calcium in the planet’s ring has been confirmed in new data beamed back from the mission’s orbital component. Such a combination of elements strongly suggests the presence (at some point in the planet’s history) of limestone. Limestone has been touted as a bioindicator, and it’s possible presence has long been suggested around other stars. Why would the presence of limestone be a big deal?

This bizarre spiral shaped volcano is a window directly into the deep history of not only TRAPPIST-1e, but the entire system.

Because here on earth, limestone is usually a biological byproduct. On Trappist-1e limestone in orbit indicates that life here once produced shells or skeletons of calcium carbonate. Perhaps the single creature spotted beneath the southern ice cap could teach us more…

What else waits in the frozen darkness?

All images ©Ben Roberts

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#Emergence in Action

The universe is a truly incredible thing. It is an endlessly cycling chaotic simulacra, churning out endless iterations of itself. The best part about being immersed in such wonder? No one needs to travel to the ends of the Universe to see this. At roughly 93 billion light years across there’s plenty to see. But the thing is, the universe is self assembling!

Yes, self assembling. What does this mean?

Exactly what it says. Nature is chock full of patterns. It’s said that nature abhors a vacuum. Perhaps it’s more accurate to say that nature abhors disorder. Patterns arise naturally from the firmament of whatever lies beneath the universe every single second every where at once all across the universe. In all of that vastness messes and disorder arise, but order always eventually spontaneously emerges.

Or at least it seems that way.

Life is a special example of emergence in action. A rather special example. It’s the most incredible phenomenon in all of existence. It’s right next to me as I write:

This is a collective of eukaryotic organisms. They all share the same genome: a special set of instructions which has emerged over evolutionary time. This set of instructions co-opts other seemingly random but very precisely designed molecules to pretty much do nothing but make more copies of itself ad infinitum. This collective of cells has organised itself into specialised structures that make the business of being a collective a little bit easier for all involved.

Now, replication of these instructions will eventually become riddled with flaws, as a process called senescence begins to emerge from this collective’s previously youthful state. Time will march on and eventually another equilibrium will emerge called death.

It doesn’t even end there. All of the atoms and compounds within this collective (from now on we’ll call this collective “Jasper”) will cycle through soil, clouds, other organisms, stars, molecular clouds, other planets and galaxies. Eventually they’ll come to rest at the end of time along with everything else. It’s a heck of a story. Really.

And all of that is self organising. Structures and patterns arise spontaneously from the laws of nature. Structures such as rivers and streams are no different to other familiar branching structures such as circulatory systems. Methane based river systems on frozen Titan resemble precisely the branching network of blood vessels that winds through your body like…..well, a river system. And it all creates itself!

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Naturally arising branching patterns on earth.

This spontaneous self organisation is ubiquitous in nature. Life , and especially multicellular life, has borrowed this proclivity for patterns, recreating those which seem conducive to biological processes functioning well.

Is this how multicellularity got a leg up?

Consider this example. Physarum polycephalum is the scientific name for a rather interesting species of plasmodial slime mold. Now, its name is a sign of things to come, meaning “many-headed slime”.

Plasmodial slime molds; not quite colonial, not quite multicellular. Image: Wikipedia

P. polycephalum breaks several tenets of what we would call common sense. Essentially, it is a single gigantic cell, consisting of thousands or millions of individual cells which have joined together for common interest. Unlike creatures like you and me, however, these cells aren’t compartmentalized like our own. In us, each cell is partitioned from its brethren by walls and membranes. The innards, including the nuclei are tucked away safe and sound. It’s truly a neighbourhood as we would understand it. Within the slime mold it’s like the sixties never died. It’s an orgy in there. All of the individual nuclei all slosh around inside this plasmodial common area. Creatures bearing this property are called coenocytic.

So. The slime mold has this kind of generic look about it, doesn’t it?

All of these structures emerge spontaneously, coded for by some as yet unknown aspect of spatial and quantum topography. I don’t know what this is, or how to elucidate it, but I know it’s there.

Life has somehow managed to encode these structures. Just like Jasper in the first image, these structures have evolved over geological time to work together, creating assemblages from which something emerges that is greater than the sum of its parts.

Could the first attempts at multicellularity have gotten a leg up? Did the laws of nature lay the groundwork for biological structures shared by the vast majority of multicellular organisms today? Consider this scenario.

Earth, several billion years before the present day. You’re drifting above a hellish landscape, in a little temporal bubble, that allows you to observe and record data but not interact with the landscape in any way. That could be disastrous. How so? Just imagine accidentally stepping on L.U.C.A; the Last Universal Common Ancestor of all life. Let your imagination do the rest. So you’re drifting along, observing, and you see something.

The earth at this time is hot. Islands of freshly minted land protrude above the semi-molten surface of a world still cooling down. You see chunks of the planet high above you, settling into a tenuous orbit. Only recently something the size of Pluto crashed into baby earth, shattering much of its outer skin and sending it into high orbit. All of those chunks you see in the sky will one day become the Moon. The collision wiped the surface clean like an Etch-A-Sketch, and so as a result baby earth is reforming again. Pockets of land like this one harbour water and other organic muck delivered by comets; the Universe’s version of Fed-Ex. Not to mention the stranger that caused all this damage in the first place.

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Space plays rough. Earth’s surface, wiped away in a catastrophic collision, provided the raw materials for its moon. Image: NASA/JPL

The view is impressive. Just imagine every vision or rendition of Hell you’ve ever seen and apply reality to it. It’s pretty cool. But something else huge is happening as well. Life is forming in the midst of this apocalypse. Your time machine hovers over the most momentous event in the history of the universe…

Whatever this tiny thing is, drifting about in warm eddies and swirls in that hot little pond, it’s the first. It may not live to see another day, or it may eventually give rise to things like you. You would love to examine it in more detail, but you ask yourself. How did this singular piece of organic machinery manage to figure out that one day forming collectives would be a good idea? Your time machine bubble thing seems to know what you’re thinking. It is only fictional after all, and the writer decides to jump forward a billion years or so….

Something large and dark slowly glides past you in the brightly lit upper layer of a sea that completely covers over three-quarters of the planet. The thing pushes you aside as a tremendous tail fin propels it down into dark depths. It’s some kind of fish. A big fish. The armour plating on its head gives it an appearance reminiscent of a tank. If Thunderbird 2 and the Batmobile (Christian Bale’s batman of course) had a baby, it would look something like this: Dunkleosteus. Your time bubble wobbles alarmingly as the behemoth sends powerful compression waves through the water. You know this is a fictional scenario, but you don’t care. You’ve gone too far forward anyway….

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Primeval earth, with a toxic atmosphere, much closer moon and primitive colonial life, in the form of stromatolites (right foreground). Image: NASA/JPL

A haze wafts across a landscape dominated by volcanic ash and a truly huge moon. Waves crash against a dark craggy shoreline. The time bubble lets you observe, but not interact, right? You can observe with all your senses. This place stinks. The shoreline is matted with a thick film of bacteria and gunk. Waves crash against the mat, breaking it up, and dispersing it further landward. You’re guessing with the moon so close tides must be insane here. This whole area is sub-littoral. Anything that can hold on here has to be tough. The rocks all give off steam. The sun isn’t as hot now as it is where you come from, but seams of volcanic activity are evident out in the water. Pillow like ridges of freshly solidified lava stretch up the shore, still not quite cool. Bacteria, or these Archean versions of them carpet some of the rocks. It’s here that you see something big. Almost as big as life appearing in the first place. Channels and rivulets run through some of the mats. Skins have formed and as water has reduced within the mats, structures have appeared. These mats have been given a push towards colonialism by the blind forces of nature. In these early more experimental times, genetic information and it’s transfer is a lot more promiscuous. A lot less Darwinian and a little more Lamarckian. These bacteria with their scrambled DNA and transfer will find this way of doing things a little easier, and will adopt it. Quickly.

Does this scenario make any sense? It does, but it had to have some basis in fact. I saw the principles in action, and they are as follows: an organic matrix, containing all manner of constituents useful to life is forced into biologically useful patterns and structures by some kind of energetic input. Where did I see this happen, or at least some analogue of it?

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My creature lives! Meet Soupenstein.

Meet Plasmodium botanicus, or plant muck. Otherwise known as puree vegetable soup. It does bear a striking resemblance to P. polycephalum, doesn’t it? This little monstrosity was created accidentally in the lab. Or should I say kitchen?

20170728_133413 It was busy. I was moving at a million miles an hour, when I spilt soup on the grill plate next to me. This odd structure was the quick result. Branching patterns and channels formed within seconds, and I was instantly taken by its similarity to a slime mold. It was this random splash that was the inspiration for this post. Now, this post is only a speculative “what if?” with some cheap time travel thrown in, but could the earliest multicellular life, or collective modes of existence have been given some kind of initial leg up by similar incidents or circumstances? There are parallels between my imagined “slime on a rock” and the soup accident above. Let’s call the soup an extracellular matrix. It is a composite substance, containing all manner of organic compounds, plus a few impurities (probably. What doesn’t?). Energy in the form of heat is applied to the ECM as it comes into contact with a flat hot surface. Water in the ECM reduces, leaving behind a concentration of material, which forms channels and branches in accordance with the laws of nature. Bacteria within this newly formed arrangement suddenly find life a little bit easier.

What of other mixes of organic and inorganic compounds? Could life have resulted from a random splash like this? Did multicellular life arise when the cosmic cook was a little busy and not being careful? It would be interesting to perform a series of experiments. Why not use foodstuffs such as soup? Would different recipes lead to different structures? Would other energy sources, or electricity, lead to new outcomes? Who knows? That’s the point of experimenting!

I’d be interested to hear what others have to say on this. Thanks for reading.

 

Ben.

References and Further Reading:

https://en.wikipedia.org/wiki/Titan_(moon)

http://www.elijahwald.com/origin.html

https://www.seeker.com/life-continues-within-the-body-after-death-evidence-shows-2212720233.html

http://www.medicaldaily.com/life-after-death-according-science-cells-fight-stay-alive-long-after-body-dies-409525

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303275/

P.S.

Thanks for reading this far! Could readers please do me a favour? I have a YouTube channel, and I would like feedback on it. If people could watch a couple of videos and give CONSTRUCTIVE criticism. What’s good? What’s not? Am I boring? Do I mumble etc? All feedback is welcome and if you can leave comments either here, on my twitter, Facebook or YouTube channel that would be awesome. I’ll make you famous. Or something. 

https://www.youtube.com/channel/UClvBq6G-DkIlKci7xXdWYzA

#OddPuzzlePieces No. 3

Death

 

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Hello and thanks for popping in today, for another assortment of random factoids. In keeping with the bone theme of the last post, things again seem to be taking a morbid turn. I’ve always been interested in taphonomy. This is the study of what happens to the body after death. More to the point it is the science of what happens to you as soon as you cease living. From a very technical standpoint, this is from the second your heart stops beating and it really is a matter of ashes to ashes. Physics and nature go into autopilot and work to recycle all the goodness that is in you. Eventually time and decay wring you dry. It’s a bit clinical, but it’s also an extremely beautiful and interesting process.

Death!

There’s much more to it than meets the eye. As a tiny green Jedi master once said, you must “unlearn what you have learned.” Forget TV. Forget it! Death isn’t as simple as pointing a gun and just killing someone:


Life isn’t so cut and dry. And that’s what this series of posts is about! In response to some of the contributions I’ve recieved this week, it seems fitting to address some random morsels of information about both Death the supernatural entity and death the physical process.

Death has had an obvious hold over us since before we were us. It is the single motivating factor that drives life on. Mythology from around the world has tried to understand it. Ancient peoples anthropomorphised death, feeling that if death was someone like us, it could be reasoned with or controlled.

Fact 1: In ancient Greek mythology, Thanatos was the personification of death. He was captured by a human criminal (King?); Sisyphus, who tricked Thanatos into shackling himself! During this period of bondage, death obviously came to no one!

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Hypnos and Thanatos: Sleep and His Half-Brother Death, by John William Waterhouse, 1874.

Fact 2: Thanatos obviously wasn’t that powerful, being defeated in a wrestling match by the hero Heracles, during his quest to rescue the princess Alcestis from Hades (the Underworld).

Fact 3: In the sacred Indian language of Sanskrit, death is a journey, or mahaprasthasana; when the soul leaves the physical body and returns to the Aatman, or Universal Soul.

Fact 4: Full skeletonisation of a body can occur in as little as month. In some cases it’s been observed to take place in one or two weeks!

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Because centuries old engravings are less confronting than images of corpses! This is a family friendly post! Deal with it. Image: Wikimedia Commons

Fact 5: There are many kinds of death, but on a cellular level there are two main ways cells die: necrosis; premature death of cells resulting from destruction which results in the cellular contents leaking out (autolysis) and apoptosis. This is a targeted sequence of genetic signals and processes whereby the cell essentially switches itself off.

Fact 6: Senescence, or ageing as we would understand it, only happens in multicellular organisms like us. It is still not fully understood why we age the way we do.

Fact 7: Cells in a dead body can regain mitotic activity, even after long periods of inactivity. This ties into…

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Many cells in the body fight to stay alive, long after death has technically occurred. Image: Pixabay.

Fact 8: Gene transcription has been observed in cadavers for some time after “death” has occured. It appears that many types of cells in a corpse actively fight organismal death. It’s like a city dying, but the individual inhabitants are still alive and kicking! (at least for a time).

That’s all for this post. There was so much from contributors that putting it all in would have turned this post into something completely unwieldy and just plain long. All contributions have been referenced and you will find links to plenty of great reading and resources below if you find (like me!) that this whole death thing is actually really interesting.

All contributors to this post found their way here via Twitter.

Facts 1 and 2 were provided by Serena:

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Fact 3 was provided by Devayani:

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Fact 4 and other interesting facts on skeletonisation were provided by Laure Spake:

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Facts 5, 6 and 7 came from a fascinating discussion with Cam Hough, a contributor to a previous post. Thanks again Cam!

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Finally, John van der Gugten brings up the rear. Again, an extremely interesting discussion was had, and there was just too much too squeeze into a post like this. Many of the links below were provided by John, and he knows his stuff. His academic page is linked to in his twitter profile, for an overview of his publications and work. Check him out!

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Absolutely feel free to leave comments or questions below. I will endeavour to hook people up with any information they may require.

Ben.

References and further Reading (highly recommended):

http://www.history.com/news/6-fascinating-facts-about-space-probe-voyager-1

https://www.seeker.com/life-continues-within-the-body-after-death-evidence-shows-2212720233.html

http://www.biochemist.org/bio/03902/0014/039020014.pdf

http://www.medicaldaily.com/life-after-death-according-science-cells-fight-stay-alive-long-after-body-dies-409525

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303275/https://en.wikipedia.org/wiki/Thanatoshttps://en.wikipedia.org/wiki/Sanskrit

 

 

 

#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.

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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.

#Yggdrassil: The World Within a Tree

“We live in a Universe that seems to be unsure of its rules sometimes. Is everything preordained, folded and tucked into the very tiny recesses of whatever quantum realm underpins our own world? Is everything an emergent property, constantly cycled and coded in real-time? Writers and thinkers have pondered this question and its countless variations since thought began. I’m not arrogant to declare I have the answers, and honestly, at this point in time could anyone? 

Whatever viewpoint you have on the universe and how it all stacks up, there are some things no body can deny. Everything works the way it works, no matter what explanation you put forward for it.”

Staring at traffic gets me in a pensive mood sometimes. It makes me wonder (as an aside) how much thinking is done at windows, watching the world rush by? Right now I’m thinking about several hours just spent at some local wetlands. Just near my home, they have been virtually rebuilt by local councils over the last fifteen years or so, in a bid to clean up the environment a little bit. It isn’t really a token gesture. The wetlands have been a beacon of success amid the constant flood of tales of environmental woe. I visit them all the time when I get time off work, and love nothing more than wandering for hours at a time, taking photos of insects and whatever else takes my fancy.

You see, I really like science. I even studied it, slogging through five years of university, so I could get a nice big certificate to put on my wall. It was fun, but I’ve realised that for me science is all about wandering around in lonely places and just paying attention to things that others sometimes don’t see. It’s all about where you feel at home, and I’ve always felt at home in my imagination.

Today’s walk took me through the Paddocks Wetlands. They’re an area set aside by local government for environmental remediation. They constitute a fairly large chunk of land, set behind factories and commercial precincts.

The open space didn’t interest me today. I was armed with a bunch of cameras and a cheap little macro lens for my smart phone. Today, I went bug hunting. I went yesterday as well, just a boy and his smartphone.

Today’s trek through the wilderness was initially not panning out. With some pretty miserable weather, insects seemed to be sleeping in that day. I was getting a little bored. I was streaming my walk on Periscope, and getting a little distracted, clowning around for the viewers.

Then, a tree happened.

Trees hold a powerful place in world mythology. The mighty Ents of J.R.R. Tolkien’s Middle Earth are derived from ancient European myth. Trees are sacred in many cultures. This probably found its greatest expression in Norse mythology, with the World Tree Yggdrasil.

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Rooted in Eurasian mythology, Yggdrasil continues its hold on modern imaginations.

According to Norse legend, Yggdrasil was a mighty Ash (sometimes Oak) tree, whose branches extended beyond the heavens into the nine realms of existence. It’s roots extended far below, into the homes of Gods and demons. I personally have always loved this tale. It’s always given trees a certain mystique. When I was younger I used to believe they could think and feel just as we do, and wondered what secrets they kept to themselves…

In a way this assumption wasn’t far off. At the paddocks wetlands today I was able to focus on a single tree, finding a host of life and drama within.

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This quiet unassuming tree became my main focus for the day.

This wasn’t just some boring old gum tree. On walking past it, I immediately noticed something I don’t see very often:

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This praying mantis, about 4 cm long was lurking quietly among some drooping Eucalyptus branches.

I was truly excited to find this little beastie. It was in the midst of eating the still twitching halves of a European wasp. It’s not every day we get to see nature at its violent best, and my camera was at the ready. The mantis was on to me, I’ll give it that. About the only important thing to heed when trying to photograph or film insects is that they are 1: extremely alert, and 2: extremely timid as a rule. They’ve been around for a very long time, and they’ve been on everyone’s menu for a long time. They’ve become very good at evading big clumsy beasts like myself. If you are, however, very quiet and move really slowly, you can get decent shots.

Or at least Twitter worthy shots.

The tree was home to so many. Dramas were unfolding before my eyes, and that was what was so great! From blood thirsty evisceration amid large gum leaves hanging like drapes to the aftermath of pitched battles:

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Sometimes, no one wins.

Yggdrasil continued to unfold before me. Fire ants were foraging in the tree branches, coming down to investigate the praying mantis. The mantis actually tossed the wasp away, on realising I wasn’t going to leave it alone! That, and the inquisitive ants coming down to assess the situation and the mantis went into lock down, assuming it’s well-known posture of supplication. As I’ve said, insects are incredible survivors. On turning away for a few moments to further explore the tree the mantis was gone forever, melting into the greens and browns of the branches drooping down to the ground.

Note: My identification of these ants may be completely wrong. Feel free to correct me. 

The ants only numbered in the dozens.  They were like a scouting party, sent from their command centre to gauge the lay of the land before invasion day. One explorer to another, I watched them go about their business.

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When going on these kinds of walks,  I have found that you can’t go out intending to find something. Most times the only times I find things worth capturing on film is when some random glance leads me to a new discovery. Even knowing where to look is not enough sometimes. Insects are extremely elusive. Their size and alertness has kept them alive for hundreds of millions of years. Like Tolkien’s Hobbits, it seems that insects and their arthropod cousins will only be seen by us big folk when they want to. This is when we go out using only our eyes to look.

One tree was full of dramas and epic struggle. A fight for survival, a loser vanquished by a stronger foe and rent asunder like a bloody trophy. The first tendrils of conquest, seeking new worlds, coming into contact with the natives. These first contacts not going so well for some; even for combatants from both sides. Perhaps there’s a lesson in that for those who care to see it.

For these tiny creatures, this eucalyptus tree was their world. Like the Norse stories, the tree was their Yggdrasil, their entire cosmology. Branches swept up out of sight into the heavens, where only the foolhardy would ever travel, risking swooping birds. The tree’s roots grasped deep, clenching around the foundations of their universe. Some branches were reaching out, entwined with those from other universes, where brave travellers would cross over, meeting inhabitants of the neighbouring universes. Unknown to them all, they were all being watched by higher powers, hovering over them.

Or, were they unaware?

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?

#Symbiosis: meeting at transitions

I’m standing on a very worn and not well maintained footpath overlooking a huge expanse of pungent sand. A mile or two out the ocean shivers and snaps in a strong midday breeze. It’s cool but the sun is putting up a fight. This place has that perfect combination of quiet, bottomless deep blue sky and loneliness. I could spend  a whole day in a place like this.

I’m here to explore a small part of the vast tracts of mangroves that crowd the coast of the St Vincent Gulf north of Adelaide. 

There are only a few places like this left in South Australia. Humanity has wrought it’s usual brand of havoc on local ecosystems, concreting and carparking the living heck out of everything in it’s path. These kinds of places are a refuge of all kinds. A refuge for wildlife and a refuge for those wanting to escape the cancerous sprawl that is humanity.

It always strikes me when I visit these kinds of places that there is a particular kind of peace here. A bizarre form of symbiosis exists between nature and the derelict fringes of civilisation  you find in these forgotten corners. To be sure, St Kilda is no wasteland: hundreds of people live out here. However, out here you see a kind of comfortable embrace between abandoned humanity and the natural world. Like tired frayed spiderwebs such old ruins hold on, degenerating somewhat to a previous natural state. 

Perhaps another term to describe this relaxed coexistence is attenuation. Out here, nature and abandoned places have become used to each other. An old shack, with it’s windows and doors long gone may be held up by nothing more tangible than the fact that gravity hasn’t really bothered with it yet. Like an old worn face these shacks sag and lean at unflattering angles, but the myriad creatures that make them their home don’t mind. 

I love finding these kinds of places, but I also respect them. They don’t belong to us anymore. They lie on some boundary which has emerged from the clash of two Orders; the human and natural worlds. We have removed ourselves so completely from nature that we forget our place in it. I watch these places fade away and see this symbiosis: a kind of neutral zone between humanity and the living world. 

These places are another kind of beast: a hybrid world, where old patterns overlay the new, and something new emerges. Even now we are beginning to see nature coming to terms with humanity in this way, as more and more species transplant themselves into our world. Birds are an example of organisms that are now thriving in the densest of human population centres. As we spread so relentlessly across the planet, do they really have any other choice?  It’s the oldest choice in nature: adapt or perish. 

These “edges”: places like the St Kilda mangroves and other regions that form transitions between humanity and wilderness will be where a true coexistence between us and Nature develops. This symbiosis could be crucial not only for our future but the future of life on this planet.