Thirty Nine Light Years: Part Three

astrobiology, astronomy, Biology, emergence, nature, sciart, scicomm

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


Beyond the Pale Blue Dot

astrobiology, astronomy, Biology, emergence, sciart

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. Such worlds are known as Ultra Short Period (USP)  planets. 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: All images © AstroAF Designs unless specified in image caption.

An Accidental Ecosystem in Space

astroarchaeology, astroarcheology, astrobiology, Biology, ecology, scicomm, science fiction, Uncategorized


I’m always interested in podcasting, and I’ve created an episode of a tentative series on the Anchor app. It’s just this blog post read out. Convenient for those whom listening is a better way to digest content. Here’s the link:

Listen to my segment “Abandonment among the stars” on Anchor:

Imagine this. It’s the distant future. Space travellers have discovered a huge structure in deep space. Let’s assume the travellers aren’t human. These beings have stumbled upon the greatest discovery in their history. A vast megastructure, hundreds of kilometres long, it’s a huge cylinder spinning slowly across interstellar space. The structure is a riotous collection of cyclinders, and other smaller structures seemingly thrown together. Tests on the structure reveal it’s very old: several thousand years at least. No signals or signs of current occupation can be found, and it’s determined after several years of examination and debate that the structure is abandoned.

An O’Neill cylinder, adrift in cyberspace.. A 3D model of a physical model I plan to build.

The very first team is sent on board…

What do they find?

The structure is derelict, to say the least. The team can safely determine this. There are no signs of intelligent life.

Mechanisms keeping the cylinder habitable are still somewhat operational. By some miracle of engineering the cylinder still has gravity as well.

But that’s not to say that life hasn’t found a way.
The structure is exploding with life!
The structure is essentially intact. It continues to rotate, driven by some unknown energy source and mechanism. It orbits a medium sized yellow star, lying just beyond the orbital path of the second planet out from this sun. The second planet is completely uninhabitable.

Image: Pixabay

There is a third planet from the Sun which seems habitable. Other expeditions are already exploring that world, and it seems this cylinder was built by whatever sentient beings once lived there.

Image source: Unknown

The structure is an oasis of life, all alone in the night. The builders may have long vanished, but the other organisms they brought on board: whether they be pets, food or pests, don’t seem to know they shouldn’t be here claiming this place as their own. It’s become an accidental ecosystem that has no business being out here and yet out here it is.


A couple of weeks I decided to do something different with all the video stuff I do. I did a livestream on facebook and periscope. The topic of my stream was the very question addressed above: what new ecosystems and organisms could arise in an abandoned, livable space station were the human occupants to disappear?


Image: Pixabay

It actually really got me thinking. The whole thing began as a random question on Isaac Arthur’s Science and Futurism facebook group. To my surprise there were a lot of great comments and ideas in response to this question.

I’ve addressed this subject matter before. A blog post explored the nature of interactions between the natural world and those sad, abandoned places on the periphery of civilisation. It’s like discovering a completely new world when I stumble upon these “transitional” places. Imagine finding such a world like the cylinder orbiting Venus. Just how and in what direction would any life on board manage?

It’s a really interesting question, and ties into the nature of life and how it has spread across our own planet. Most life existing today hasn’t arisen spontaneously from the firmament. Nothing’s done that for around 4 billion years. No, life has migrated, hitched rides or been tossed about by catastrophe and happenstance. It has essentially gone where the wind blows, and taken root wherever it has landed. The theory of panspermia relies on this vagrancy to offer an explanation for how life might have appeared here in the first place. I personally think Panspermia is very plausible.

In some ways we’ve seen panspermia in action, from a certain point of view.

This is of course, a very tenuous observation I make, but the principle is the same, using the example of Ascension Island in the Atlantic Ocean. This tiny little mound of dirt popping up from the waves is a giant ecological lab, an ongoing experiment that began over 150 years ago. All manner of species: some introduced, some native, were thrown together, on a barren little rock. Within decades, the island was a lush green paradise, with new ecosystems and new equilibriums. Quite amazing really, and Ascension Island represents a window into the greening of a dead planet such as Mars.

So. To return to the premise of this post. Explorers find a derelict space colony, now overrun by non human life. We’ve seen this on Earth too. Life is especially good at exploiting new niches. When the dinosaurs perished, the mammals that had lived in their shadow for 180 million years suddenly had an entire planet all to themselves. This resulted in the Tertiary radiation, a speciation event rivalling the Cambrian Explosion in the profusion of new species of mammal that suddenly appeared to exploit all this open space. Disaster ecology is an area of study devoted to this knack life has of adapting to catastrophe and finding new balances. Places like Ascension Island are one example of this. Others, like Chernobyl, are another.

03-Chernobyl-animals.ngsversion.1493139603170.adapt.676.1 (1)

Life is doing nicely in the radiation soaked wilderness of Chernobyl. Image: James Beasley and Sarah Webster, National Geographic Creative

So what of my superstructure, adrift in orbit around Venus? It would take several posts to really give it some justice, and so that’s what I’m going to do. A few posts on the post human world in a self contained semi functional space colony.

I must admit I have not been active with this blog lately. I have been busier than usual with new work and things in personal life shifting and changing constantly. It’s never forgotten. This will be attended to, and posts are going to start going up on a more frequent basis. Stay tuned, keep reading and I’ll be writing soon.


Europa: Life Beneath the Ice?

astrobiology, astronomy, Biology, Biomolecules, scicomm, solar system

The Chicken and the Egg


There’s an old theory known as Panspermia,  which hypothesises that life got its initial leg up on Earth (around 4-3.5 billion years ago) after a long journey across space. According to this theory, (which at the very least is quite reasonable) the ingredients and precursor molecules for life hitched a ride on comets and asteroids and reached earth early in its history, when these objects impacted our planet. As for where these molecules and ingredients came from…well, that is a real chicken and the egg type question, and one I will be exploring in more detail in future posts as well as videos.

Not all astrobiologists agree with this of course. Each to their own. Science and seeking the truth is all about disagreement. I’ll leave the debate alone and for the purpose of this post assume that Panspermia is a pretty valid idea.


You said it Neil. Funny thing is, look at all the people agreeing with him. Kinda ironic?


This post (and the YouTube video it will eventually give birth too) is essentially a piece of speculation. Looking into the future of space exploration, what is waiting for us out there?

Europa has been the hearts desire of many an astrobiologist for decades now. Ever since the Pioneer 10  probe rushed past back in 1973 and sent back the first pictures it’s been a bit of a rock star. Why? Because it ticks a whole lot of boxes on the “Things could live here because…” checklist.

Things could live here because….

Let’s look at some of those boxes. And why they’re important. First of all:

1: Europa is  now widely believed to harbour a substantial subsurface ocean: of actual honest to gosh water. How have we come to this conclusion?

Take a look at the surface of Europa.

It sure is striking. Huge channels and streaks criss cross the moons frozen exterior.

And that’s about it.

No craters? Callisto is part of the Jovian family as well, and is the most heavily cratered  object in the solar system. Compared to Europa Callisto is a teenager with weapons grade acne.

Like an explosion in a pizza factory.

Europas surface is geologically new, having been resurfaced recently (in geological terms). Something is wiping the slate clean on Europa, and this is our first clue that Europa is special. Something under that icy shell is acting upon the surface and rearranging it.

Astrobiologists think it’s water. A lot of it. Europas surface is basically a shell of ice, rafting and fracturing like pack ice on Earth. Essentially vast swathes of pack ice remodel the Europan landscape and are thought to be it’s version of our plate tectonics.


2: Some time ago, none other than the venerable Charles Darwin postulated that life began in a “warm little pond”, whereby the right combination of mineral salts and energy resulted in the first biomolecules. Ever since this first speculation, forwarded in a private letter from Darwin to his friend Joseph Hooker in 1871, science has placed an emphasis on water as the likeliest birthplace of life on Earth. Darwin believed in a warm little pool, many other theories have thought bigger, fingering the ocean as the culprit. Whatever the case may be, and whatever supporting evidence gives testament to it, water (for now) is the one thing no life can exist without.

And Europa has a lot of it. The deepest point on our planet lies at the bottom of the Marianas Trench, some 12 kilometres below sea level. That is deep to be sure, but the abyssal plains of the world’s oceans are on average about 4 kilometres beneath the waves. Europas subsurface ocean averages a cold dark 62 kilometres deep!

Where do the minerals fit into this? Patience, grasshopper!

Jupiter pumps out extremely high levels of electromagnetic radiation. This is, of course, a constant engineering hurdle for the various missions that have paid the gas giant a visit. It’s extensive family of moons: some 67 in total are constantly immersed in this field, which interacts with various bodies in various ways. Europas magnetic field is no different,  and is an induced magnetic field.  This is a special kind of magnetic field produced when an electromagnetic field is passed through some kind of conductive material. In the case of Europa this material is believed to be an ocean, brimming with conductive mineral salts. Such an ocean would be a vast salty brew, fulfilling Darwin’s vision somewhat.


Europa’s magnetic field changes in relation to it’s position within Jupiter’s magnetic field, indicating it isn’t generated by the moon itself, but is induced by Jupiter.

What of Darwin’s energy source? To understand this a little more, and to see what it means for Europa, we need to understand that all life requires an energy source. On Earth, the vast majority of life is solar powered. What does this mean? You can’t just go outside and photosynthesise! You need to go to the fridge and get a snack. Food keeps you going, right?

Absolutely. But where did that food come from? Whether  you’re a vegetarian or a carnivore, ultimately every single thing in that fridge of yours exists because of the sun. Either it grew from the ground, something came along and ate it, or something bigger came along and ate that something. The sun is at the base of this very simplified food web, and it’s been doing it forever of course.

No solar power is not some fandangled idea. Renewable energy has been around, well, since before life began. The sun provides energy not only for Earth’s climate and hydrological cycle, it also fuels all photosynthesis on Earth. Plant life not only provides food and oxygen for animal and fungal life, it also contributes to climatic processes.  Yes, the Sun is really important.

Ah, you think, how does any of this relate to Europa? The frozen moon is a bit further out from the sun than warm little earth, at about 485 million kilometres. Not much use for solar power out there! Well it turns out that not all life on Earth is completely dependent on the Sun after all.

Enter the hydrothermal vents.

These are exciting and mysterious places, home to a bewildering and diverse array of lifeforms. They are found where life seemingly has no business existing, and yet there they are: on the vast abyssal plains of the ocean floor. Miles away from any sunlight, subjected to pressures and extremes that would kill us instantly life thrives in a hostile alien world.


A white smoker, situated at the Champagne Vent in the Marianas Trench, Pacific Ocean. Image: NOAA

These ecosystems are based not on photosynthesis, whereby sunlight is converted into a food source for plants, but chemosynthesis. Down here life has found a way, to steal a phrase from “Jurassic Park”. Literally, bacteria have evolved to survive at the hellish temperatures and pressures around these hydrothermal  vents, where the water can reach temperatures of over 350 degrees Celsius. With nothing but a rich mineral brew spewing from these vents out onto the ocean floor, these bacteria have learnt to make use of this brew. These bacteria then form the basis for some of the most intriguing ecosystems on the planet. These vents are an oasis of life, all alone in the abyssal night.


Concept art showing the possible structure beneath the ice. Image: NASA/JPL

Does Europa have the capacity for such vents, far beneath the ice? On Earth, the vents are geothermally heated. Earth posesses a core of molten iron, heated by slow radioactive decay of elements from the formation of the planet 4.6 billion years ago. This internal heat eventually reaches the upper mantle of the planet, seeping through in more threadbare regions of the Earth’s crust,  Europa is heated by Jupiter itself. As the moon orbits the gas giant, tidal forces act upon it, squeezing and massaging. Resulting frictional forces are believed to sustain a heated core, which, just like earth, could provide energy to keep systems of hydrothermal vents running on the abyssal plains of Europa.

So. Europa may tick some really important boxes, for the existence of life. Water: definitely check. Minerals and organic compounds: check. A source of heat, to power possible life: check.

Now the only thing for it is to visit; to get through the icy shell to the ocean beneath….

To be continued….

Next post takes a ride beneath the ice.

17th November 2017:

And here is the video for which this post formed the script:


Further Reading and Resources

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#Emergence in Action

astrobiology, astronomy, Biology, Biomolecules, ecology, emergence, Molecular Biology, nature, scicomm

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!

2017-03-06 16.28.34

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.


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….


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?


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.



References and Further Reading:


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.

#OddPuzzlePieces No. 3

Biology, Biomolecules, folklore, Molecular Biology, mythology, nature, scicomm




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.


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!

Waterhouse-sleep_and_his_half-brother_death-1874 (1).jpg

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!


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…


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:


Fact 3 was provided by Devayani:


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


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


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!


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


References and further Reading (highly recommended):





Biology, Biomolecules, nature, Proteins, scicomm

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



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.


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.”


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 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.


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?


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


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.


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.


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?


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.



#Yggdrassil: The World Within a Tree

Biology, ecology, emergence, entemology, folklore, insects, mythology, nature, scicomm, science fiction

“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.


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.


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:


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:


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.


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?

#DNA: What’s the Deal?

Biology, Biomolecules, Molecular Biology, scicomm

It’s 2017. We’re three sequels into a massively successful movie franchise about the dangers of science without integrity. Rebooting and endlessly recycling movies doesn’t seem to be a problem, but who cares about that?

Four huge movies about science. Naughty scientists playing God. Evil money hungry corporations sacrificing principles in their endless cancer-like quest for growth.


Grow, my little economy, grow!!!

Nope. Still doesn’t sound familiar? This sounds more like a day on your facebook newsfeed, right?

“Jurassic Park”! At it’s core, this was a tale about the difference between knowledge and wisdom. Scientists who should have known better, and knew the right choice to make ignored it in the quest for money and recognition.

What else was this movie (and it’s progeny) about? Breaking it down into it’s scientific sub-units, “Jurassic Park” was a story about serious genetic engineering. Scientists manipulated and recreated ancient DNA, enabling them to bring back creatures that hadn’t seen the light of day in at least 65 million years. As it turned out, these creatures and the twentieth century didn’t get along so well. The rest you know. If you don’t… watch the movie. On a personal note “Jurassic Park” was one of the last “Oh wow!” movies I saw. The first time that Brachiosaurus appears, it sent shivers down my back.

Remember the scene when DNA was reduced to a friendly cartoon character, something like that old Microsoft paperclip?


Ah, Clippy…

I’m showing my age. Keep reading. Is DNA really that malleable and user friendly? Students and many scientists probably don’t really get the amount of work that went into determining 1): that it exists in the first place, 2): how it works and 3): it’s structure. If you’re this far into this post you most likely have a more than passing interest in science and molecular biology. You know about Rosalind Franklin, Watson, Crick and Wilkins, and various other big hitters in the vast field that is molecular biology.

Like most others I garner things I need to know from textbooks or the internet. All of this information is piled atop older information, blood, sweat and tears. After all of this work, wouldn’t we know enough to be able to create prehistoric GMOs? No. Absolutely not.

One thing that strikes me about DNA, and about life itself, is that within all organisms, across all arenas and Domains of life lies a universal genetic code, evidence of our common ancestry. This code; this cosmic language has given rise to literally all life on this planet. There are a couple of anomalies here and there, but they can be ignored for the sake of this post. Here then, is the Genetic Code:

Adenine, Thymine, Guanine and Cytosine.


You’re tapping your fingers, I know. Your’re waiting for the rest. There isn’t any more. This is the genetic code. Four bases. Often they are reduced to mere letters, and so appear more like a simplistic alphabet. Combinations of these four “letters” comprise the genetic machinery of all life, coding for enzymes, hair, fins, wings, organs, blood vessels, immune systems, bad breath and low IQs.

That’s really it! Four bases, code for all life in all it’s forms. It’s an astonishing feat not only of information storage, but of fidelity of said storage. In nearly four billion years of life on Earth, only 10 percent of the original genetic code has become corrupted, resulting in all life other than simple unicellular organisms. That’s right. Putting it another way, you and me are the result of slight signal degradation. Ten percent doesn’t sound slight! It sounds like a lot! Over 3.5 billion years however, for the original genetic code to degrade only 10 percent is the kind of signal fidelity communications engineers have funky dreams about.

DNAs information storage capabilities are a function of that groovy double helix shape it winds itself into; a result of various molecular bonds inducing this spontaneous double helical twist. A DNA molecule is essentially two molecules; two strands of intertwined de-oxygenated ribose nucleic acid.


Somewhat resembles a twisted ladder, doesn’t it? Image: Wikimedia Commons

See the “rungs” in the middle of that twisted ladder? They are where the magic happens. These comprise various combinations of the aforementioned bases: Adenine, Thymine, Cytosine and Guanine, joined by hydrogen bonds of varying strength. The bases attach to nucleotides, which are then fused to this sugar-phosphate backbone. In this way they are safely tucked away, wrapped in loving embrace.

The bases don’t just stick together. As mentioned, they are held together by hydrogen bonds of varying strength. Hydrogen bonds are a common chemical bond found in nature. They are quite weak, but form spontaneously when compatible sub units are positioned appropriately. Adenine bonds with Thymine, forming two hydrogen bonds. Cytosine will only pair with Guanine, forming three hydrogen bonds. To repeat, Adenine will only bond with Thymine and Cytosine will only bond with Guanine. This forms the basis of Watson-Crick base pairing, and is the only way bases will pair in DNA. Complementary base pairing is the mechanism by which DNA strands form, and allows new strands to be created later (to be discussed in a future post).

It also makes a pretty neato U-Beaut exam question, and a real gimme if you’re struggling. After all, knowing the above rules: A to T and C to G, you can determine the sequence of a strand of DNA if you have the sequence of it’s opposing or anti-parallel strand.

I won’t ask you to try it!

Future posts will look at DNA replication, including an examination of the mighty ribosome, one of the funkiest biomolecules around. Please feel free to comment on this post and share it with others. See you again- real soon!

Enzymes: Nature’s Toolbox

Biology, Biomolecules, Molecular Biology, Proteins, scicomm

Enzymes blow me away, and really do speak of some kind of underlying order in the Universe. I mean, you can’t just study enzymes and their activity without thinking there’s some kind of voodoo at work. When I was young (and even occasionally in these adult years) airplanes would fill me with wonder. I mean, we know how airplanes work, but it still seems somehow magical. Something that big and , well clunky just has no business flying. It’s like that old chestnut about bees. Yes, we know they have no business flying but they just do.

Enzymes have that same mystique. They are catalytic proteins which enable a vast array of biochemical reactions and processes to take place. Without these little worker bees swarming around inside us DNA is useless. After all, DNA may be biomolecular royalty but the French Revolution taught us what happens to royalty when no one’s listening: it becomes surplus to requirements.

Enzymes are thought to work in two main ways. Both avenues are a function of shape. All proteins perform functions tied into their conformation. Over 30000 proteins are known to exist, with a bewildering array of structures: knots, crazy tangles,  wheels, hooks, and just about any other shape you can imagine. How is shape important, you ask?

Do you ever dive into a tool box to perform basic household repair jobs?

Not tools, functional shapes. Image: Pixabay

Pop quiz! Your university graduation certificate has fallen off the wall, causing  your cat to jump twenty feet. After you’ve peeled the cat from the ceiling you need to get the hook back into the wall. Do you grab:

A): A screwdriver

B): A banana

C): A hammer

D): Laundry detergent

Smartass remarks aside, you grab the hammer. Why? Because the hammer has  a very particular shape which turns out to be just right for banging small things (nails) into bigger things (walls). The hammers job is a function of its shape. It doesn’t really stop there. Analogous to proteins; which have been evolving and changing for billions of years hammers are the result of centuries of engineering and refinement. After all, if you were in a hurry or just plain lazy you could have hammered the nail with any heavy object (lucky the cat’s out of reach right now). However,  something heavy like a book would kind of do the job, but it would have limitations. It may not fit in your hand well. It may rip when being slammed into the nail. If it’s a soft cover book it may absorb the energy of impact. It’s width will impair your view of the task at hand.

Get the picture? A hammer circumvents all of these limitations.

You hammer the nail back in and hang your certificate back up. Your cat is having a bad day. The hammering has driven it over the fence and into the neighbour’s yard.

Other tools in your toolbox have very particular functions closely tied into their shape or design. So it is with proteins.

A 3D representation of Myoglobin. Image: Wikipedia

The crazy whorls and loops in myoglobin allow it to be a particularly effective binding pigment, which attaches to iron and oxygen. Found in all mammals it only appears in humans after muscle injury. It appears in higher levels in ocean going mammals such as whales and dolphins, which often dive for extended periods, allowing them to remain submerged.

Protein chemistry and function is surprisingly interesting, but falls outside the scope of this overview. A youtube video briefly explains enzymes and how they work.

Proteins are perhaps more astonishing given that they aren’t alive. Yet, they tirelessly perform myriad functions within living things, allowing a signal of life to emerge from chemistry and metabolic white noise.
If you find proteins or other biomolecules interesting, which ones interest you? Interesting comments may form the basis for future blog posts or even youtube videos. Leave a suggestion for the biochemical employee of the week!