Friday 30 June 2023

life II

 Hello Daddy?

How did life first come into being from a dead piece of organic matter?  With this quest in mind, I went forth and reviewed the relevant material and literature from diverse sources. Although serious scientists have applied their scientific and analytical skills for about 70 years now, the results have proved disappointing. From my cursory review, it seems that numerous research groups throughout the world are on the brink of a significant breakthrough. And then I looked back to work conducted in the late 1990s and several research groups working then stated they were on the cusp of a significant breakthrough........

It is to be remembered that conditions on early Earth c3.5 billion years ago were vastly different to today. The atmosphere of that time contained little or no oxygen. This primitive miasma was dominated by the presence of carbon dioxide, water vapour, methane and other trace gasses. Of course, this primitive atmosphere would be noxious and lethal to present-day organisms. The majority of today's creatures, great and small, rely on oxygen for their respiratory metabolism (aerobic). Oxygen levels in our current atmosphere are around 20% and are maintained by organisms utilising the power of photosynthesis. Oxygen is necessary for aerobic respiration, and clearly, the very first life would have had to rely on other means for energy generation.  

The RNA World 

What follows is a highly truncated and simplistic review of how the RNA world is thought to have formed       

All researchers in the field agree that the first life formed in a watery environment. This environment c3.5 billion years ago would be a soup of organic compounds formed from ubiquitous carbon. There are several energetic events that could have been responsible for the synthesis of organic compounds from inorganic molecules. Lightning strikes and thermal energy from volcanoes would have done the trick. At the time of the 'Great Bombardment', meteorites containing organic compounds would have covered the primaeval Earth. It matters not whether the first life appeared in a warm muddy pool or on the ocean floor next to a volcanic vent, there is a fundamental paradox that must be tackled, the ultimate chicken and the egg question. Chains of nucleic acid molecules (RNA and DNA) are required for self-replication, however, this replication can only occur with the help of proteins consisting of amino acids. Both types of molecules are necessary for the propagation of life. What came first, nucleic acids or proteins? Both are required and act in unison for the process of replication. It is hard to imagine that these two exceedingly rare events could happen spontaneously. Perhaps religious folk are correct after all, and a god(s) is/are required to provide the vital spark. One solution relies on the properties of single-stranded RNA molecules. According to this hypothesis, RNA strands act as a template for their own propagation. This process would have to be facilitated by other RNA strands that have folded upon themselves, an innate property of certain RNA strands. These two separate systems would have to spontaneously engage and cooperate to facilitate the replication of single RNA strands with high regard for fidelity. It is to be imagined that open RNA strands would continue to replicate in a milieu of organic chemicals. Competition for free-floating ribonucleotides would then occur. A form of chemical evolution would ensue and ensure that the fastest replicating molecules would dominate and therefore drive the formation of an efficient cooperating replication system. The problem with such a free-floating system is that the replicating RNA strands would be at the mercy of other molecules within the system that might destroy the growing and replicating RNA molecules. Researchers agree that some form of enclosed protective canopy would have had to develop fairly early on to offer some form of protection. Organic lipids in water will spontaneously form spheres. This is due to the molecules having both hydrophilic and hydrophobic regions. That is, one end of the molecule will attract water molecules while the opposite end repels water. The result is that lipids in a watery medium naturally form 'fatty bubbles'. Somehow, the primitive RNA system (I refrain from calling this life) would have had to enter the protective lipid sphere. From there on, the structure would continue to absorb free-floating ribonucleic acids, and the system would continue to replicate. And then, at a suitable time, a portion of the RNA system would bud off and still remain enclosed within a portion of the original fatty domain. And so on, and so on. This model assumes that chemical evolution would drive these primitive systems to become better at replication and at acquiring substrates. Therefore, along the way, most of these competing 'bubbles' would succumb, and at some fine juncture, there would emerge from this chemical deluge a single system that goes on to be refined by natural selection, finally becoming the 'organism' that goes on to beget all life on Earth. If this is the case, then when did the lipid bag of nutrients actually become life. This is moot, I suspect it is analogous to asking when did the first human arise from our ape-like ancestors. Could we actually define a moment and pronounce with absolute rigour/vigour that a particular individual was fully human? And how would we categorise the status of the parents? This proposed continuum presents us with a problem. Could there be a defining moment in the history of our planet when chemical evolution transformed and became life? There is much to ponder here. Of course, all this is pure conjecture, and there are numerous problems with this model. It would be necessary for all the elements to come together almost simultaneously for all this to be feasible. Each step borders on the impossible. The probability that each step in the process could come about and interact stretches probability to unknown realms and, dare I say it, borders on the miraculous. With all that said, it must have happened somehow. The fact that I'm able to sit here and write these words whilst scratching an itch on my twinkle should be testament enough. 

My attempt at explanation is an extremely truncated affair- how could it be otherwise. Also, my limited exposition is only one scenario of how life could have come about. There are alternatives, although many rely on some form of RNA initiation. These alternatives will have to wait another day. 


Thursday 29 June 2023

An Old Soldier's Tale

Some Folk Collect Stamps....

I've nearly completed part two of my composition about 'How Life Began On Earth', and hopefully, barring a calamity of dynamic proportions, this post will emerge tomorrow unfettered. Therefore, as an interlude, I will regale my loyal readers with an anecdote concerning my dear departed paternal grandfather. This one is for you, Charles Percival, you nasty irascible dead bastard.

I was rummaging through a drawer the other day in my expansive 'Master Study' when I noted a faint cloying odour. I couldn't place it for a second, although it tugged vaguely at some deep-seated memory. I removed the drawer containing the evocative olfactory stimuli (steady Flaxen, ya starting to wax again) and tipped the contents onto the shag pile. I peered intently at the mound of detritus and shiny things...... And there it was coiled provocatively around an empty container of 'Tic Tacs'. A dishevelled/shrivelled collection on a brown string- twas Granddad's old ear collection, which he bequeathed to me in his will. As I recall, it was: item number 6. Not so much grisly as gristly. I hadn't seen them for a few years, but they hadn't changed much. Twenty-seven ears, all pierced dead centre and threaded onto old-fashioned brown waxed string. Time had not been kind to this assorted allotment of grizzled pinna. Over the years, they had folded upon themselves and taken on a distinct, dark amber hue, very reminiscent of a 'pork scratching'.   

When I was young, my father, bless him, when in his cups, would regale me with lurid tales about his father's wartime exploits during the Great War and would hint darkly about a mysterious relic which never left Granddad's waistcoat pocket. So I was aware of the 'Ear Story' but put it down to old soldier's tales. And so the years passed, and old Gramps finally passed away. His meagre collection of goods was distributed amongst the relatives. My cousin inherited my grandfather's gold fob watch on a silver chain, and I got item number 6 secreted inside an old cocoa tin. And who said the old cunt didn't have a sense of humour.

I never really knew my wicked old Granddad. I can't recall him ever speaking to me directly or taking the slightest interest in me. Which is just as well as he spoke an archaic form of the 'Black country' dialect, which seemed to use few actual English words. My most vivid memory of him was his eyes, which were piercing and bright china blue.

Of course, it is nothing new for soldiers to take souvenirs from the battlefield. My dad had a couple of cap badges and a bugle with a bullet hole taken during the Korean conflict. But old gramps had an ear collection and had passed them on to me as a dark joke. I have considered burying them, but I confess, the ears hold me in their macabre and ghastly thrall. A legacy is supposed to be something to cherish, and it is the only physical item I have to remind me of the nasty miserable old twat. I did notice that some of the ears were collecting a black speckled mould, which I cleaned off with 70% ethanol. So, after a quick spray with air freshener (mountain dew) and a quick rub down with a chamois cloth, back in the drawer, they went.

Uncannily enough, my own son resembles my Grandfather quite closely, even down to the same shade of blue eyes. Therefore, I thought it only fitting that once my span has run its course, I should pass on the family 'Heirloom' to Flaxen Junior. I will have to put an explanatory note in the old cocoa tin otherwise, he might just throw the ears away. Tis a Flaxen tradition, after all. 

My son has had a prior acquaintance with the lugs. Once when he was but a pup, he managed to find the ears in a cupboard. Foolishly I had forgotten to put them back in their 'coffin' after an inebriated fond fondle. Thus encumbered, my 18-month-old son promptly shoved them into his maw. He was enjoying a good chew and had made a good account of ear number three when his mother showed up. Oh, she did laugh. And that is why, to this very day, I sport a scar across my noble temple.

Wednesday 21 June 2023


   Don't Ask A Physicist

In today's post, I'm writing about something that I actually know about, and that is biology. I am not saying I'm an expert on all the varied topics that make up this most wonderous of subjects. That would just be silly. But at least I have spent a reasonable amount of time in a formal educational setting studying many of the diverse areas that constitute the condition that is 'Life and all that Entails/Entrails'. And at least in one arena of the subject, Human Genetics, I could be considered an expert- whatever that means. Although, I do confess I'm a tad rusty on the rapidly developing technology these days. The point of this diffuse ramble? In this post, at least, I don't have to pepper my introduction with caveats and limitations as is my wont when dealing with topics outside my sphere of expertise. I'm not saying that this post is error-free. But I am saying that my errors are at the very least, informed errors. With the caveat, so stated, allow me to write anew/askew.         

Life, the great mystery:- I've approached this ultimate puzzle, previously, on this very blog, and from several directions. And indeed, there is much to ponder. In today's post, I'm taking a fresh and wry look at the ultimate question.  

Let us look back to when the primordial Earth came into existence 4.6 billion years ago. At birth, and for at least a billion years into its infancy, our planet was a mass of seething, roiling molten rock. During this time the primal Earth was subject to numerous asteroid impacts making the surface extremely bestrewn and chaotic. The energy imparted by these impacts helped to maintain the molten state. It was during this tumultuous era, that a Mars-sized mass slammed into the Earth sending a lump of molten debris into space. Once cooled that 'debris' would form our only Moon. Eventually, the great bombardment would cease and the Earth's surface would cool sufficiently to a point where life could form without the hindrance of 'Thermal Insult'. This occurred about 3.8 billion years ago.

In the scorching interior of Australia, there can be found mounds of fossil bacteria laid down 3.5 billion years ago. This represents the earliest evidence for the presence of living organisms. Thus, we can state that life was certainly present just 300 million years after our world had become 'quiescent'. Now, this might seem like a long time interval but in terms of geological history, this is but a blink of a ferret's eye. And, when we examine the fossil evidence relating to this early organism it is obvious we are already dealing with a well-evolved bacterium suggesting that life on Earth had formed many million years previously. 

So, how did the first life come about? The quest to uncover how life formed from non-life is a post for another day. Hopefully, I will be able to publish, on this very organ, within the next few days, about the thorny problem of Abiogenesis.

But before I begin to tackle this most vexing, and most fundamental of inquiries I would like to jump forward, a step, and address and be propelled to consider the following question, namely, how do we define life? What are the characteristics of life that distinguish it from non-living stuff? This is a deceptively difficult question and it will be useful to contemplate the problems that arise when we try to grasp this particularly slippery ferret by the tail (Flaxen, steady with the incipient waxing, especially ferret waxing). From first principles and intuition, it is relatively easy to list the properties that life, may, or must have, to 'exist'. Students during middle school biology classes are usually taught the acronym MRSGREN, which represents: Motion, Respiration, Sensitivity, Growth, Reproduction, Excretion and Nutrition. Even from a cursory glance, it is clear that not all living things are so well-endowed. Of all these characteristics, a few stand out as universal. Thus, ALL living organisms, irrespective of phyla, must have a means of propagation, regardless of whether it is asexual or sexual, or both. Also, a means of collecting energy, or manufacturing energy, is a universal feature amongst the living. The other characteristics, so stated, are negotiable and dependent upon the biological complexity of the creature in question. For instance, mammals appear to be endowed with the entire collection of life's dynamic qualities. At the other end of the spectrum, viruses, appear to be equipped with nowt, apart from reproduction. And yes, I'm well aware that not all biologists think that viruses constitute life. I'm not going to squeeze into this particular lagomorphic hole today. And anyway, I've already written (x2) about this subject- go seek and be amazed!

Is life special?- this might appear to be a stupid question, but the answer is elusive on mature reflection. Erwin Schrodinger, he of quantum dynamics fame, reduced life to its ultimate base state and described 'life' in terms of the Second Law of Thermodynamics. Simply stated, this law describes the flow of energy in enclosed systems. Inevitably, the flow of energy in any enclosed system has a spontaneous tendency toward disorder (entropy). Thus, Schrodinger explained life as an enclosed system that harnesses energy to reverse the process of entropy. However, the laws of the universe are not to be trifled with, or denied, and once the organism expires, the inexorable process that is entropy proceeds unhindered. Therefore, this decisive and reductionist definition of Life can be explained tersely and as follows: A transitory suspension of the Second Law of Thermodynamics within a closed system. Do you find this definition a valid description of 'Life'? Well, this definition is not an exclusive property of life. There are myriad examples of inanimate objects disobeying the entropic principle, albeit for a little while. Consider the car in your garage, for example. What about a guttering candle? And so the list goes on.  

There are those, often embued with a mystical quality, who think that there is an ethereal spark that induces the inanimate to become animate. This mystical force is synonymous with the concept of the 'soul' (perhaps). A force field that is present but departs upon death to go elsewhere. Religions, various, are rather keen on the idea and have been so for millennia. Christians are supposed to take heed of the eternal soul. It used to be thought that the soul was the sole property of Homo Sapiens and that lesser breeds had to make do without. And yet modern genetics has shown that hubristic humans are not that much different from many of the supposed 'lower species'. Even the humble mollusc, especially those of the class, Cephlopodia, have shown traits that we consider intelligent. The 'Soul Concept' is essentially a philosophical question outside the domain of scientific study. Although, I will say, there is absolutely no scientific empirical data to support this notion. Take it as you will.  As said, my next post will consider the question of how life first came about. This is enough for today.