Category Archives: Molecular Biology

#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.

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




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!

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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!

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):




#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.

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

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!