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#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.

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#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. 

#BackToVenus

It’s 12.13 a.m. I’m watching the end credits for “Doctor Strange” roll off my TV screen. The house is quiet of course, but I’m still wide awake- as is my norm. Twenty two years working in kitchens has turned me into a nightowl.

Personal Aside: Has anyone else seen that second little end of credits scene in this movie?

Anyway. Because it’s late, I’m thinking of material for my next YouTube video, and am dumping a whole pile of pictures of Venus into Adobe Premier Pro; my video production software. All of these thumbnails are arranged in a disorderly mess before me, calling me to the second planet from our Sun. It’s a fascinating place, and I have been in a real Venus mood for the last few months.

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So close to Earth in so many ways, and yet so alien. Image: NASA/JPL

A Hell born of Paradise

Venus is a dead world like it’s unfortunate sibling Mercury. Both planets are perilously close to our sun. Mercury lies only 58 million km from Sol and Venus is still uncomfortably close at 108.2 million km. However this cloud coated beauty orbits serenely on the very inner cusp of what astronomers call the “Goldilocks Zone”; that mystical band within which temperatures are mild enough for water to remain liquid on a planet’s surface. To our knowledge, only Earth possesses water in this state; although water is actually abundant in the Solar System. A previous post: Water, water everywhere explores this in more detail.

For Earth, the porridge is just right. Venus is a little too close: too hot, and Mars is a little distant: too cold. Venus today is a blistering, scorched wasteland, where on a cold day the temperature is a hellish 460 degrees Celsius and the atmospheric pressure at “sea level” is 92 times that on Earth. Put it this way; if you were standing on the surface of Venus it would be equivalent to being 1.6 kilometres under the ocean.

From a compositional point of view  Venus is very similar to Earth, and in fact the two have been referred to as sister planets.

The Evil Twin?

Venus, thy name is dichotomy.

Venus and Earth are remarkably similar in terms of mass, gravity and composition. Note: composition can only be gleaned from inferences made by measurements made of the planet’s density, but there is a general consensus that Venus and Earth are quite similar in this respect. Structurally Venus is also believed to be kin to Earth, with a rocky crust about 50 km thick and a core of metallic iron, believed to be in a liquid state.

Venus: mass, volume and gravity in comparison to Earth. Image: Wikipedia
A sunburnt Pacman.

Ok, some people say. So we know Venus is obviously not that similar to Earth. Cut to the chase, Ben. Why can’t we go there?

Good! I was waiting for someone to ask that! Even if it was an imaginary reader!

Venus is nasty. Venus is a bad place. Perched in a nearly perfect circular orbit around the sun (itself unusual) Venus should just scrape into the habitability club. Some scientists even believe that Venus once was covered with oceans and continents. Just imagine it!! Fly over those oceans with your mind. Leave the CGI and the billion dollar special effects to the big hitters in Hollywood and YouTube land and join me..

Was this Venus a couple of billion years ago?

 

A long time ago, on a planet not so far away….

It’s morning. You’re on ancient Earth, circa the early Archean Period. Your clock is useless because the days are much shorter. You throw it outside your time machine (any design- it’s your imaginary ship!) and get some breathing equipment slapped over your face. The Great Oxygenation Events haven’t happened yet and won’t for a long time. The atmosphere is not much fun: consisting of mainly methane and ammonia. Fun and games if you’re one of the extremophile microorganisms slowly spreading across the Earth. Not so much if you’re a human from the twenty first century.

Keep that breathing equipment in good shape. You’ll really need it where you’re going.

Artist’s impression of Archean Earth. How close is that moon?!! 

Well, ancient Earth is nothing if not picturesque,  that’s for sure. No harm in taking a few photos before you embark on your voyage out to Venus.

Archean Era Earth: beautiful one day,
And bombarded the next.

Time to go.

Your little ship skips across the void in no time. No special effects budget can out maneuver imagination! You can’t help but fidget as you approach earth’s sister:

Venus looks decidedly different to how it’s represented in twenty first century textbooks and media. The all enveloping shroud of thick sulfuric acid clouds isn’t blanketing the planet. That’s a relief. An atmosphere somewhat similar to the one you left behind  on Archean Earth is here. Atmospheric pressure seems to be tolerable. Are those clouds you see, wafting across a vast equatorial ocean? Your face is pushed so hard against the window of your tiny spaceship you’re about to crack the glass. Decompression NOT FUN. You better go down….

At this juncture in the history of Venus (right now it’s not even 1 billion years old) the planet really could be called Earth’s twin. A shallow global ocean swirls gently, glinting brilliantly in the afternoon  Venusian sunlight.

Afternoon of course is a meaningless concept here. You look at your clock again, and clench your teeth. Again it’s useless! Why did you bring it?

Because you’re a character in this tale and the Author (that’s me) thought it would be a cool plot device, allowing the reader to see how days and years have changed- both on Earth and Venus- over billions of years. You jettison the clock for real this time. No one is ever going to find it.

A day on on Venus is equivalent to about 234 earth days. That’s right. On earth someone would ask you the time, to which you might reply “11.30”. On Venus a correct response might be “half past April.” As if that’s not bizarre enough, the year here is 225 Earth days long. That’s right! A year is shorter than a day here!

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ProtoVenus: quite earthlike?

The planet really is earth-like. The planet has a messy, turgid magnetic field. In a few hundred million years that field will be gone. Some kind of event has taken place (or will take place) that basically is a killing blow for the planet and anything that may live here. For now the magnetic field is allowing liquid water to pool on the surface- lots of it too.

You’re standing on some charred volcanic ridges, looking out over a still, glassy ocean, which glints in the sunlight. No waves crash against the walls. Venus has no moon. No moon, no tides. This ocean is more like a still lake, filling shallow volcanic plains between the planet’s three main highland regions, or “Continents”. In the distant future scientists and missions to Venus may have detected the presence of granite down here on the surface. Granite is found in huge quantities on Earth, and forms in the presence of both water and tectonic activity.

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A world of mysteries, Venus beckons..

The atmosphere is clearly substantial enough for liquid water to be stable. You’re dipping your toes in that water right now! Is anything alive here? You feel a pang of loss for this world. Looking out across this nameless ocean it really seems plausible that right now things are oozing or eating their way across some shallow seabed somewhere, competing for resources which one day will be gone, choked in sulfuric acid clouds and incinerated by oven like heat and pressure.

Earth has had a handful of truly epic extinction events. The greatest extinction event of all is responsible for the rise of almost all modern life. A pollutant began appearing in our atmosphere. It’s ironic that perhaps the most lethal pollutant every pumped into our atmosphere wasn’t carbon dioxide or methane. It wasn’t hydroflurocarbons.

It was oxygen. That’s right. 

Cyanobacteria appeared, spreading quickly across the globe, producing free oxygen as a metabolic waste product. Unfortunately  all other life on earth at the time was anaerobic; meaning they didn’t require oxygen for their metabolism. When cyanobacteria began to massively outcompete all other life, oxygen levels both in the oceans and earth’s atmosphere reached saturation. Almost all life on earth perished.

At this point in time you can only guess what’s out there in that Venusian sea. Isn’t it fun to speculate though? 

It’s time to suit up and fire up your time machine. 2017 is waiting for you, and a world straight from the fevered imaginings of some tortured 16th century poet awaits you….

Welcome back!

Next time, let’s wander across Hell.