Thursday 30 December 2021

Endosymbiotic Theory in all its Glory

This is the last post for this year of 2021. And let's face it, twas shit (the year, not the post). Moving on.....

In this post I would like to bring forth for contemplation the, 'Endosymbiotic Theory' first brought to light in the 1960s by a biologist, Lynn Margulis. But before considering the theory in a more depth, I'm required to delve into a little background information for the edification of the soul.

It has been estimated that the Earth is 4.54 billion years old and life appeared perhaps as early as 4.3 billion years ago. First life on Earth would have been very simple, single-celled organisms. Evolution for the next 2.3 billion years would result in a vast array of these relatively primitive, single cells. The bacteria we see today are the direct descendants of these simple cells and are classified as prokaryotes. It would seem that life would have continued along this rather happy-go-lucky, primitive pathway but something wonderful happened which kick-started evolution on a new and exciting trajectory......... 

Consider our primitive earth 2 billion years ago. Within the oceans lurked life, but not life as we know it today. Evolution occurred, albeit slowly, and as always modified form and structure; a process in perpetual motion. As previously mentioned, life at this time in our evolutionary history consisted of unicellular organisms without the power to construct complex multicellular structures. Power is the key, or more importantly energy. Energy expenditure is what defines life and distinguishes the world of 'life' from 'non-life'. These simple bacterial forms produced energy by a means known as glycolysis. I'll not go into the cycle itself (many years ago I had to memorise this cycle, and many more. Arse). Suffice to say, that this energy-generating pathway is responsible for keeping entropy at bay. Entropy is a fascinating subject in itself. Energy, if left to its own devices, is always winding down to a lower, less organised state incapable of performing further useful 'work'. Remember, energy can never be destroyed only changed. Energy is the life giving chameleon of our world, and indeed for the entire universe. Have I digressed?

Sometime 2 billion years ago a single bacterial cell engulfed a much smaller bacterium. Tis a bacteria, bacteria eat world. Normally the larger organism would digest the engulfed bacteria thus extracting life-giving nutrients. But for some reason, lost in the eons of time, on this occasion something unique and singular occurred. Instead of destroying the hapless bacterium, the larger cousin, by means and mutations unknown encouraged the reproduction of the organism within its cell. The larger cell then began to nourish and nurture its much smaller brethren. The benefit for the larger cell is that it began to feed on the surplus energy provided by the inclusion. The larger 'host cell', in turn, provided a protective environment for its tenant. The smaller of the two bacteria would eventually evolve into the ubiquitous organelle, mitochondria; also known as 'The Powerhouse of the Cell'. This situation, where both organisms obtain benefit from their intimate association is known in biology as, mutualism. The first 'complex cell' (eukaryote) was formed. The fact that this event happened, only once in life's complex evolutionary history is attested and elaborated by modern genetic analysis. The surfeit of energy enabled the evolutionary development of more complex, interacting/cooperating, multicellular organisms.  It is sobering to reflect that all complex life, including humans, owe an evolutionary debt to this rather aberrant mutated 'mother cell'. This event may have implications for the formation of complex life elsewhere in the universe. Could it be that our inability to contact other intergalactic civilisations is because they don't exist due to this fundamental hurdle on the pathway to complex life?

There is another point to be made. Bacteria reproduce by asexual means. Therefore genetic diversity in these organisms relies on the production of mutations. In contrast, multicellular organisms reproduce sexually. This allows for an increase in genetic variability- the fodder for evolution to digest and work on. Therefore, evolution occurred quite rapidly in these first eukaryotic cells eventually resulting in the plethora of multicellular creatures we see today. It is interesting to note that for 2.3 billion years, life remained single-celled and primitive. Thereafter, with the formation of eukaryotic cells, it took only 2 billion years to produce the vast array of complex life we see today, thus is the evolutionary power of sexual reproduction. Consider the fact that for the majority of the time that life has existed on Earth, the only organisms alive were bacteria.

It seems that in addition to this initial endosymbiotic event, sometime later in evolutionary history, a second engulfing occurred in a cell already playing host to mitochondria (can you actually have two unique events- only on this blog?). Therefore, mitochondria were not the only organelle to make this jump to existence within another cell. These cells would eventually become part of the great, 'plant kingdom' and the inclusion would evolve into the organelle, called chloroplasts. Chloroplasts contain the necessary chemical apparatus for photosynthesis a feature associated with all living plants, with the exception of the parasitic forms.

Both mitochondria and chloroplasts still contain certain primitive elements characteristic of their bacterial ancestors. They retain their own DNA, which is organised in a circular form, just like modern bacteria, and produce their own proteins. Both organelles have also retained the ability to reproduce independently within the 'host' cell in an asexual manner, again this is a trait shared by bacteria.

These incredibly rare evolutionary events are responsible for the rich complexity of life we observe on Earth today. Without these critical associations, life today would be no more complex than a smear on a rock, in the ocean. Makes you thunk, dun it?


Friday 24 December 2021

Flaxen's Christmas Felicitations

Shagger says: "Buy me a pressie or I'll bite your bollocks clean awf

Tis Christmastide in the Flaxen abode. All is well with the world. Peace and harmony have descended throughout like a descendy thing. The snow lies deep, crisp, and even. The sparrow forages in the hoar frost for a tasty tidbit. The wolves in the hill howl a cry of hope. The sleeping child lies upon the crib, moist, warm and free of care. The log fire crackles and throws a warm glow throughout our humble abode. Choristers sing out in harmony upon our doorstep. The light from their multitude of candles cast a guttering glow that alights their ruddy cheeks in rubicund delight. The eggnog flows free and the mistletoe hangs in expectation above the incandescent hearth.....

Is it Bollocks!

The cosy/rosy picture painted above, of course, bears no exactitude to reality. In truth, the weather is a balmy 30 degrees, thus negating the log fire. No rosy-cheeked cherubs bestrew our deck with song; no wolves either. Fuck eggnog, it tastes like shit.

Let's be frank, the past year has been particularly shit and one that mankind will gladly see its demise with gleeful abandon. COVID has ravaged mankind. The economic cost has been incalculable, and still, the infection continues unabated.

At the personal level, fortune has been mixed. My health remains indifferent as I contemplate the fact that over the past 12 months I have become an opiate addict. On the other hand, the archery business I started with number one son continues to grow and our intention is to expand into the large Australian market.

The family will gather today. My son and girlfriend will arrive from the windy city. My mother will be joining the throng this year if her health holds. Presently she resides in the local 'granny farm' which caters to her multiple health issues. My daughter, and her family, already live with us and hopefully in the near future will move out to start a new life living on an old school bus. Four people crammed into a single-decker 1980s bus- surely, nothing could go wrong, could it?

Christmas day will be predictable. Hearty morning breakfast followed by the opening of the pressies. Later in the day, we will partake of a conventional Christmas dinner of turkey, lamb, and ham followed by Christmas pud and custard.

Anyway folks, I wish you a good hearty Christmas festival and I will pick up my mighty pen in the New Year and write anew. Let us hope that 2022 is a whole lot better than the year we are leaving behind- good riddance say I!

Merry Christmas and Happy New Year from the Flaxen Family.      

Tuesday 21 December 2021

Dark Forrest

I've considered the Fermi Paradox before on this blog. A simple search will expose the post in all its magnificent glory. For those that can't be bothered I will outline the main details: We have now determined that, in our Milky Way galaxy alone, there are billions of planets (some 7 billion earth-like) orbiting other suns capable of supporting life. Given that the universe has existed for 13.8 billion years we would expect that life has evolved many times on many of these exoplanets. It is reasonable to expect that conceivably (highly likely?) there will be alien life forms more technically advanced than ourselves. In fact, it is not inconceivable to consider our galaxy, and by extension the universe, to be teeming with intelligent life. But even though we have been actively 'looking' for intelligent life for 70 years or so, we have found absolutely no evidence to suggest intelligent life is 'out there'. In essence, this is the Fermi Paradox in stark simplicity.

Various solutions have been proposed to explain this most vexed of paradoxies. The Great Filter: Mayhap there is a 'barrier' preventing the formation of advanced civilisations. There are several possibilities. Life on Earth can be divided into two domains, prokaryotic and eukaryotic. Bacteria are good examples of prokaryotic cells and all multicellular organisms are eukaryotic. Bacteria are less biologically complex than eukaryotic cells. It has been hypothesised that the evolution from prokaryotic life to eukaryotic occurred only once in evolutionary history. The evidence for this hypothesis is very convincing and in the near future, I'll generate an article outlining its importance and significance for higher life. The biological complexity of eukaryotic cells allows the formation of multi-cellular organisms ultimately evolving to intelligent life. It has been argued that this original mutation is incredibly rare (?almost impossible). Could this be a valid explanation of the paradox? Or maybe there is a more sinister explanation. Perhaps civilisations in the cosmos are very like us and have destroyed themselves by war or by the exhaustion of essential resources. Regardless, it is possible to theorise a number of 'filters/barriers' preventing the formation of highly advanced extraterrestrial life forms capable of intergalactic travel.

Another theory for consideration is the so-called, 'Dark Forrest. Perhaps the universe is teeming with intelligent life, but the sensible civilisations are lying low and quiet. Consider the following scenario: We know that an essential element faced by all life on earth is competition. There is a limit to the number of useful resources in a given environment, this fosters competition, not only within species but between species as well. This competition for resources is an important driver of evolution. Humans are here because our ancestors were aggressively competitive and modern humans continue to be so. It is known that modern humans coexisted with other humanid species, Neathandels being the most prominent and well known. However, all these human-like species eventually became extinct and by 10,000 years ago Homo Sapiens was the only species left in the great arena of life. It is likely that Homo Sapiens out-competed their brethren either indirectly, or directly, or more likely, both. There was only one niche available and the more aggressive, and perhaps the more intelligent species prevailed. Competition within our species is a constant. History is replete with instances of more advanced civilisations coming into contact with lesser developed societies. The outcome is inevitably catastrophic for the 'lesser breeds'. It is innately ingrained in the human soul to take advantage of others to their ultimate detriment. Anthropologists used to have a rose-tinted view of our pre-history ancestors as pacific individuals living in peaceful harmony with others. Recent archeological data has shattered this rather naive picture of ancient man. Evidence has become available showing mass graves with individual skeletons exhibiting obvious marks of violence. Inter-human violence is a ubiquitous quality of mankind- ain't dat the sad truth.

There is no reason to expect that alien civilisations have not been driven by similar aggressive principles. This assumption is crucial to understanding all life at the fundamental level. Evolution is driven by selective forces acting on individual organisms. In fact, tis inevitable. These selective forces, all other things being equal, will result in the 'most fit' organism passing on its genes. It is conceptually useful to consider living organisms as vehicles for the storing and passing of genetic information. Ultimately it comes down to genetic transfer to future generations. Success or failure is dependant upon how well the genetic storage system is at reacting to the myriad of external elements impinging upon the system. Some folk take exception to this extreme reductionist viewpoint as it takes all the romance out of life. Nonetheless, DNA cares not a jot for our pathetic emotional debris and detritus. Success is only achievable and sustainable over the corpses of others. Therefore assimilating and taking these fundamental principles into account perhaps it is best, for humanity, to lie low and not attract attention from potentially hostile, expansionist, and predatory alien species.

Of course, because evolution favours the development of base aggressive instincts, it does not necessarily mean that aliens will react negatively to others in the great wide cosmos. Humans pride themselves on their ability to control their atavistic, primitive impulses/instincts and to formulate a humane and empathetic demeanour. These qualities set us apart from all living things, with a possible couple of exceptions. Is it fair to suggest that a highly advanced technical alien species would be so disposed? Would you be willing to bet your life on it? Perhaps the alien life form would be so advanced that our feeble attempts at technology could be conceived as unrepresentative of life worthy of their contemplation? Why not bat us aside as we do a fly?

This brings us back to the Dark Forest theory. There are only two types of technically advanced alien civilisations 'out there': the quick and the dead. The universe might be teeming with life, but no one is advertising their existence, just in case....... But what happens if we do detect an alien civilisation? In reality communication with an alien civilisation would be the speed of light. The cosmos is a vast arena and it is likely the aliens would be many light-years distant. Perhaps they have advanced enough to warp space and time. In theory, after the initial communication, they would be able to travel to our system almost immediately, if they so chose. In that case, we might expect benign, friendly contact, or an invasion fleet. Imagine the panic engendered as the world leaders contemplate their options. Certainly one of those options might be a preemptive strike as they materialise within our solar system. Come out blasting and damn the consequences.

Seriously, in such an eventuality, there is much to contemplate. We may be worrying unduly. Am I being unduly pessimistic and/or simplistic? Perhaps we are the only intelligent species in our big wide universe and that this is the best outcome for our species. What do you think?

Tuesday 14 December 2021


                                                 The measure of man?

In 1901 an American Christian physician, Dr. Duncan MacDougal, set out to prove the existence of the soul, experimentally, by weighing patients at the time of death. His rationale revolved around the possibility that the soul had a finite weight that could be measured. At the time of death, the soul would depart and the loss of weight could be recorded.

There is much that can be said about this experiment and none of it is good. To enlightened folk 120 years later, the experiment appears naive and misguided. We need to remember that at this time in history, even well-educated folk, were likely to believe in God. Atheism, as a concept, would only take hold, in the West, after the Great War. What I find particularly strange is the concept of the soul as envisaged by the good doctor. The notion of the soul, in the West, has undergone much change over the past 2,500 + years. It can be traced from its early beginnings in Greek thought (Homeric-pre-Socratic) to a thorough exposition by the great Greek ancient philosophers, Plato and Aristotle. Their concept of the soul heavily influenced philosophers to come ultimately becoming incorporated into  Christianity by the early Church Fathers. Thus our modern idealisation of the soul is essentially 'Ancient Greek' with a modicum of Christian garnish/varnish. Curiously, the theology of the soul as outlined by the ancient Jews did not overly influence the Christian concept. I find this interesting, as of course, much of what we consider 'Christian' has been taken from Judaism (?discuss). I think it would be worthwhile to write on the topic of: 'The Concept of the Soul, in the Western Tradition', at a later juncture. Anyway, for the purpose of this post, it is sufficient to note that the Western concept of the soul has, to the best of my knowledge, always been considered as an ethereal incorporate entity and therefore devoid of mass. As such, it would not be expected to exhibit 'weight' as a constituent property. Therefore, conceptually, MacDougal's experiment was very much at odds with 'theological thought' of the time; very curious indeed.

Clearly, the logistical problems involved were formidable. But this did not deter the doughty, indomitable Dr. Duncan MacDougal as he embarked on designing a foolproof protocol.

Dr. MacDougal managed to obtain six patients on the point of death. He persuaded his moribund patients to lie on a modified bed containing a sensitive scale. At the time of death, Dr. MacDougal noted any change in the patient's weight. His conclusion: the weight of the soul is equivalent to 21gms. However, this result was obtained from only four of his dying patients and the data obtained was inconsistent.

This experiment has been cited by Christian groups as scientifically proving the existence of a soul even though the experiment assumes and implies that the soul has a physical manifestation, counter to mainstream Christian doctrine. The good doc repeated his experiment on fifteen dogs. In this instance, there was no loss in weight at the time of death. Dr. MacDougal considered this result in accord with current Christian doctrine. Only humans were exalted enough to be worthy of a soul. All other living organisms, and inanimate objects, were bereft. There is no mention of how the canines expired. I can only surmise that the 'good doc' helped the dogs to relinquish their grasp on existence with a little morphia.

There is so much wrong with MacDougal's experiment that it is difficult to know where to start, although he did manage to get his findings published in a respectable medical Journal (American Medicine 1907). Criticism was leveled soon after publication and very few scientists and physicians considered MacDougal's findings valid. Ultamately only four patents provided data in this study. This is a ridiculously small sample set to base such wide-sweeping conclusions and it is impossible to perform any credible statistical analysis. On this basis alone the experiment can be disregarded. It is only recently that we have developed techniques to define and measure the precise time of death. The criteria used by MacDougal to determine the exact time of death was considered flawed and imprecise. It has also been argued that the means to weigh the patients was not accurate and only precise to 5gms. At the time of publication a prominent American physician, Dr Augustus Clarke, proferred a more probable cause of weight loss following death. He stated that at the time of death there is usually a sudden rise in body temperature causing an increase in sweating resulting in water loss. As dogs have no sweat glands they would not exhibit a corresponding loss in fluid at death.

I see no need to belabour the point. Although a small group of fundamentalists might be convinced, the vast majority of serious scientists, and lay folk alike, remain unconvinced. As far as I'm aware there has been no subsequent attempt to repeat the experiment, on human subjects at least. Given the immense logistical (and ethical?) hurdles involved, it will come as no surprise. And frankly, serious physicians, and scientists, have better things to occupy their research time and budget. 

As a passing sentiment, I will leave my faithful readership with the following prose.

      My Soul. I summon to the winding ancient stair;

Set all your mind upon the steep ascent,

Upon the broken, crumbling battlement,

Upon the breathless starlit air,

Upon the star that marks the hidden pole;

Fix every wandering thought upon

That quarter where all thought is done:

Who can distinguish darkness from the soul?

Saturday 11 December 2021

Flaxen Saxon having a bit of a Ramble......


What is science? This is a real, meaningful question for today. Although most folk claim they understand 'science' at its base level a quick chat with the average citizen will reveal very little meaningful comprehension. Science literacy is important, even for none scientists, and should, in my opinion, be emphasised at an early stage in our education. Perhaps the science curricular could acquire time slots allotted to ridiculous topics such as 'Gender Studies'. I will send a quick missive to the 'National Education Dept of New Zealand.' I'm sure they will be receptive to my erudite recommendations. Arse.

Even scientists can become confused with the base core that is 'Science'. This is not because, at the fundamental level at least, the principles are overly complex. The problem lies in the fact that the underlying principles of science are never put forth in a coherent way. Even at the university level, there is a deplorable lack of teaching directed to imparting the basic essence of scientific endeavour and practice. It is assumed that these underlying principles will be miraculously absorbed by an undefined method of 'intellectual osmosis'. However, it is well worth the time to formally teach the importance of scientific endeavour, the underpinning principles of science, and methodology at an early stage in a pupil's education.

There has always been folk in society that have eschewed science and scientific principles. A host of reasons can be put forth. Science is often at odds with accepted religious practice and doctrine. Those whose religious will and austerity are unyielding will oft side with their particular brand of religious doctrine/indoctrination to the detriment of their scientific understanding. As a good example, it is worth considering the teaching and societal status of 'Evolutionary Theory' in the United States. The theory of evolution has been around for 170 years and is still considered the best explanation for change and variation within and between species, Nonetheless, fundamentalist Christians dismiss the principle as 'just theory' and incompatible with their religious teachings. Sadly, and according to the latest polls, 40% of the American public believes in creation. This statistic is shocking. This level of scientific ignorance should not belong to a modern industrialised country in the 21st century- but there it stands. Arguments put forth by fundamentalists are laughable and ludicrous. Tis clear that many have not performed their due diligence in reading the primary evolutionary literature. Their comprehension of the topic is obtained from the pulpit and literature from other religious apologists. Their arguments are easy to refute and rebuff thereby exposing their underlying ignorance.

It has to be acknowledged that our paltry human brains have not evolved to deal with the complexity of the natural world. Our brains evolved in a particular environment. An environment full of atavistic danger. We needed to contend with the presence of large predators physically stronger and more adept than us. Disease via microbes assailed our fragile bodies and natural selection favoured a sophisticated and effective immune system. The selective pressures we encountered as a species were not geared to produce a mind capable of comprehending the complexities of our world at the fundamental level, and this shows when we attempt to deduce valid descriptors of reality. Science, by necessity, works with models that approximate or imitate reality. We seek reality but that reality is elusive. Our understanding lurches on as we discover new knowledge that is in accord with our current model of reality. If the observable data doesn't fit, or frankly contradicts our model, then the model requires modification or abandonment. Generally, science progression comes slowly in small packets. It is only rarely that we observe a seismic shift in our understanding. Einstein's theories of relativity supplanted the Newtonian model of reality and today is considered the best model we have to explain time and motion. However, lately, there have been some worrying contradictions suggesting that Einstein's Model is not quite correct. Mayhap will have to await the arrival of another prodigal genius to put forth a more accurate theory.

It is also acknowledged that science doesn't have the answer to all our questions. As stated we can only approximate. This is, of course, manna to the religious. They deal with absolutes. There are no doubts. At least no doubts religious leaders wish to impart to the 'simple believer'. Thus the Iman and the Bishop preach absolutes; there is no room for doubt. Leave doubt to the scientists. The charlatan likewise plays the same game of certainty. Notice that the snake oil peddler is oft to present their product as a 'miracle cure'. In contrast, legitimate medicine rarely makes 'cure-all' claims. For instance, there is no one treatment that is effective against all the cancers that assail our wretched bodies. Yet many will be taken in by chicanery of emotive words, such as 'Natural Products' or 'Lost Ancient Wisdom'. These buzz words fool millions and even the highly intelligent are not immune to such blandishments. Consider the case of Steve Jobs: he was diagnosed with cancer eminently treatable, and with a high cure rate, by conventional medicine alone. Modern Western medicine is based on hundreds of years of accumulated scientific data and knowledge. No arcane wisdom is needed. Anyone can pronounce they have found a cure (insert any disease you desire) on the basis of sound marketing. No empirical clinical trials or painstaking clinical research is necessary. It is often considered a virtue if the elixir of life does not conform to conventional wisdom and contains no synthetic compounds. It is as if the simple mantra, 'natural' is always good and synthetic is always 'bad' is actually meaningful and true. Jobs thought that alternative, so-called 'natural treatment', was the pathway to a cure. He was wrong and he suffered the ultimate penalty as a consequence. Many find these absolutes attractive and comforting. Science can do no such thing. Science raises doubts, not absolutes. Religion and charlatans offer an endpoint; science contemplates a journey. A journey where the destination is largely unknown. Consider the extent of the scientific journey that has been traveled over just the last 200 years. We have come far.

Scientific advancement and the acquisition of meaningful knowledge is a matter of approximating gradations. For instance, the model of the atom we learn at school is not the model contemplated by the professional physicist. Atoms can't be balls of matter and strings of energy at the same time. String theory is perhaps our most complex and intricate model of reality. But scientists, if they are intellectually honest, accept that the model is incorrect. While it unites much of what we know at the quantum and macro level it is becoming clear that it is not consistent with all our observations. Scientists are human after all and like everyone can become irrationally attached to an idea or notion; hubris is universal.

There is much incomprehension and ignorance, by lay-folk, concerning the methodology of the scientific method, its power, and limitations, that I'm tempted to undertake a series of posts, hopefully illustrating and illuminating these important issues. Let me know in the comments whether you think it would be fruitful for the flaxen-haired one to pursue such a course.