Category Archives: Biomolecules

Images of Astrobiology

The universe is turning out to be a more interesting place with each passing day for me. It’s not all about reading research articles and trawling the internet for interesting news in the vast field that is astrobiology.

I’ve been working on images related to various themes in astrobiology. This field really is a playground for the imagination, and it has something for everyone….

Recent news of a relic subsurface biosphere just beneath the surface of Mars…

Our ones and zeroes formed in starlight?

Something really special here: possible traces of limestones found in the fragments of objects orbiting a nearby white dwarf star…

 

Differing definitions of the Habitable Zone further push the limits of life in the universe..

Svante Arhenius, a swedish chemist and early pioneer of the theory of panspermia..

Ruminations on the code (codes?) that make life possible. How many languages does life have in the Universe?

Does the chemical rich, pitch black seabed of Europa host life? Does that of Enceladus?

 

The first image I created. I hope you’ve like these. There will be more! By the way, the background for this image comes from an online simulator called Goldilocks, by Jan Willem Tulp. His work can be found here. It’s really cool.

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Europa: Life Beneath the Ice?

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.

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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.

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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.

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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.

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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

http://geology.com/stories/13/life-on-europa/

https://en.wikipedia.org/wiki/Panspermia

http://www.whoi.edu/page.do?pid=83497&tid=7842&cid=70453

View story at Medium.com

https://blogs.scientificamerican.com/thoughtomics/did-life-evolve-in-a-warm-little-pond/

http://ffden-2.phys.uaf.edu/webproj/212_spring_2015/Amir_Raz/amir_raz/Magnetic.htm

https://cosmosmagazine.com/space/hunting-the-building-blocks-of-alien-life?utm_content=bufferc7d0e&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

View story at Medium.com

View story at Medium.com

View story at Medium.com

View story at Medium.com

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

View story at Medium.com

View story at Medium.com

#Emergence in Action

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

Yes, self assembling. What does this mean?

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

Or at least it seems that way.

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

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

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

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

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

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Naturally arising branching patterns on earth.

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

Is this how multicellularity got a leg up?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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My creature lives! Meet Soupenstein.

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

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

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

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

 

Ben.

References and Further Reading:

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

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

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

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

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

P.S.

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

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

#OddPuzzlePieces No. 3

Death

 

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

Death!

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Facts 1 and 2 were provided by Serena:

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Fact 3 was provided by Devayani:

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

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

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

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

Ben.

References and further Reading (highly recommended):

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

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

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

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

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

 

 

 

#SignalDegradation

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

 

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

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

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

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

 

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

He told us the tale of life….

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

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

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

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

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

Freak accident.

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

Life.

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

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

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

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

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

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

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

Moving on Ben.

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

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

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

Keyword: Reading.

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

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

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

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

Hah!

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

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

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

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

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

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

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

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

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

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

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

Maybe not.

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

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

 

Ben.

#DNA: What’s the Deal?

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.

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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?

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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.

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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

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.

https://youtu.be/tmXQoVPgq5w

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!