Thursday, 9 August 2018

LUCA and Other Musings


Recently I had a discussion with a young Jehovah’s Witness. The discussion soon turned to evolution and it became very clear to me that my young protagonist had no idea concerning the mechanism of evolution. No surprise I suppose as the JWs are only allowed to read texts about evolution that have been penned by the JW hierarchy and these texts exclusively emphasise how evolution is not a valid driver for biological change, thus paving the way for creationism. He had been taught that scientists believe that man had evolved directly from the great apes such as gorillas and chimpanzees. Actually, this is a misconception held by many lay folk and is not exclusive to JWs. This is not how evolution works and I explained that humans and great apes were derived from a common ancestor loping about some 6 million years ago. Humans and apes then diverged to pursue their own unique evolutionary histories and pathways culminating in modern humans and modern apes. He had never been taught or had contemplated this scenario before and appeared genuinely nonplussed.

Not only do we share a common ancestor with the Pongids, but by extension, to every other living creature on earth, even the humble Prokaryote bacterium. Prior to 1977, life could be classified as belonging to one of two domains: Prokaryotes and Eukaryotes. Prokaryotes refer to bacteria, Eukaryotes are more complex multicellular organisms and this broad domain includes creatures as diverse as fungi and humans. In 1977 the science of Taxonomy broadened to include a domain subsequently classified as Archaea. Archaea are single-celled organisms, vaguely similar to bacteria, but simpler. At some point in evolutionary history, the three main domains converged and consequently shared a common ancestor. Is this mere conjecture from biologists indulging in a drug filled reverie or is it evidence based? The genetic revolution over the past 40 years has allowed scientists to gain access to genetic evidence suggesting a common ancestor to all current life on Earth. A comparison of the genetic blueprint from diverse species enables geneticists to check for gene commonality. Genes have been discovered which appear in all species so far examined. It matters not that it be a bacterium, toadstool or human, these genes are always present. The implication, of course, is that these universal genes arose from a common ancestral organism or: Last Universal Common Ancestor (LUCA). Also, genetic technology enables researchers to reach back to uncover the genetic makeup of this mother of all life. A putative genomic reconstruction suggests that LUCA was sustained by 500 to 600 genes.  Furthermore, it is likely that the ancestral genome was RNA based. All living organisms extant are DNA based. DNA is a much better molecule for the conveyance of genetic instructions and for the faithful reproduction of information. However, DNA is a more complex molecule than RNA and the first life is more likely to have started with simpler molecules. The evolution from RNA to DNA based life forms would have represented one of the major milestones in the development of life.

LUCA represents a very primitive form of life and may have existed some 3.8 billion years- only 700,000 years after the formation of the earth. This is not to say that LUCA was the ‘first life’. It has been hypothesised that other life forms were present, but LUCA represents the organism which spawned all life we see today. Other competing life forms were ultimately unsuccessful and have disappeared, without a trace. Earth’s environment 3.8 billion years ago would have been completely different from today. First life would have arisen in the oceans and LUCA may have flourished next to geothermal vents on the seabed. Metabolism would have relied on and exploited chemical reactions in the sulphur rich environment. The development of photosynthesis harnessing sunlight and carbon dioxide to produce energy while releasing oxygen as a waste product would have to wait for a further 1.8 billion years. Cyanobacteria were the first organisms to utilise solar energy for photosynthesis. They flourished in the warm shallow waters of the continental shelves. At that time the atmosphere would have been composed of a highly reducing atmosphere of carbon dioxide, methane, ammonia and water vapour. Over the next 200 million years the highly successful cyanobacteria released oxygen thus changing the atmosphere to a more familiar composition with an oxygen level of around 20%. Oxygen is a highly reactive molecule and most forms of life could not adapt to this highly oxidising environment culminating in the Great Oxygenation Catastrophe. Most forms of life perished thus setting the stage for the radiation and evolution of life based on the successful cyanobacteria.

For me, the evolution of early life is a fascinating topic, but not as interesting as the original formulation of life itself. When we find evidence of early life in the rocks, that life is already highly complex and highly evolved. But going further back in time, what constituted the first ‘life’? And more importantly, if the first primordial life could somehow be resurrected in a ‘Mad Scientist’s test tube or surreal dream, would we recognise it as such? Now that IS a question.        


Wednesday, 1 August 2018

Aristarchus of Samos

Aristarchus of Samos wallowed in this world circa 310 BC to 230 BC. A philosopher not quite in the mould of classical philosophers. Aristarchus, like Archimedes, embarked on what would be called today: ‘Scientific Endeavour’. He is the first to present the heliocentric model that placed the sun in the centre of the known universe. This was in contradiction to the widely held view, famously put forward by Aristotle, which placed the Earth at the centre of all celestial bodies. The Earth-centric model was further developed and mathematically refined by Ptolemy of Alexandra c150 AD, from which it takes its name (Ptolemaic System). Thus, Aristarchus’ heliocentric model remained an unpopular explanation for the near cosmos until the coming of Copernicus who showed the scientific validity of the heliocentric system (1543) in his book, ‘On the Revolutions of Heavenly Bodies’. Nicolaus Copernicus, to his credit and rightly so, ascribed the origin of the model to Aristarchus. Of course, the works of Copernicus and others heralded the coming of the ‘Scientific Revolution’, a most remarkable and scientifically fecund period in human history- I’ll have more to say about this period in a future post. The evidence for a heliocentric system could have been divined by any genius during the Medieval period had it not been for the Catholic church. The Church effectively stifled contemplation along these lines. Anyone, suggesting a non-Earth ascendant model risked the designation of heretic as it was considered contrary to ‘Holy Scripture’. Copernicus’ model did not immediately receive Papal censure possibly because Copernicus posited the model as a hypothesis and couched his thesis in a way to suggest it was not necessarily true. Also, it was a difficult time for the Church as it was heavily involved and distracted by the 'Council of Trent' (1545-1563). During this period the Church was grappling with the devasting implications of the Protestant Reformation. With time, religious opposition mounted and the book was placed on the list of banned books 73 years after publication.
We have little of Aristarchus' work from his own hand and most of what we know about this presciently modern thinker is derived from the pen of others, especially Archimedes. This is unfortunate as other writers rarely go into detail as to Aristarchus’s deductive thinking. Therefore, it is not known whether Aristarchus arrived at his revolutionary system by intuition or whether he used astronomical observation and mathematical reasoning to thrash out his model. I’m inclined to the latter explanation as it is known that Aristarchus was an accomplished mathematician and astronomical observer. 
Sadly, only one of Aristarchus’s works has survived. Here he attempts to calculate the sizes of the sun and moon. He also makes a heroic attempt to calculate the Sun and Moon’s distance from the Earth by observation. From this, he calculated that the distance of the Earth to the Sun was 19 times greater than the distance to the Moon. Although his result was incorrect this was due to the limitation of observation technology of his time. His methodology and deduction were faultless.       
And there we have it. Poor Aristarchus has never received the recognition he undoubtedly deserves. In ancient times this was probably due to the unpopularity of his theory as it clashed with the musings of the balefully influential, Aristotle. In  modern times he has gained a mere footnote in the annals of history and most folk today are oblivious to this ‘Great Man's’ achievements. 

Sometimes history can seem unfair and capricious for reasons often dimly perceived or perceived not at all. But this is no bother to industrious Aristarchus- his consciousness has long since disappeared and posthumous fame can count for nought with the dead. 

Sunday, 29 July 2018

Women, beware of men bearing lists!

Tis a hard road to find the perfect woman
Let’s be honest finding a suitable mate is not an easy proposition in any age or culture unless you happen to belong to a culture where the parents pick the partners. Although the process can remove much of the stress involved in finding and courting a mate it is likely that you will end up marrying your first cousin. From a biological perspective this is not a wonderous proposition and if continued with gusto over generations there is a likelihood that the offspring will start regressing along the evolutionary ‘Tree of Life’.  If you want children with more than the biological requirements of toes, then this may be the right decision. Makes it easier at mealtimes. Just hang them upside down in the nearest convenient tree and pass the bananas. On the downside, the single eye in the centre of the forehead does not make for perfect binocular vision- might drop the bananas.
When I was a lad, courtship was an extremely fraught affair. It meant dressing up in bell bottom jeans and cheesecloth shirts and hitting the local disco after forcing down half a bottle of Sherry. Now, this was a time during the early 70s when the music genre of ‘Glam Rock’ was rampant. Tis a most forgettable era for music. Adherents used to wear their hair long and plaster their faces in garish coloured makeup, and this was just the men. Imagine the disco scene: Laser and strobe lights snaking out in a darkened smoky atmosphere. Loud throbbing 70s music and sweaty gyrating teenagers. My opening move was to solicit a suitable female for a dance. Getting the gender correct was the first hurdle to negotiate, for reasons already mentioned. Certainty could only be achieved by a strategic grope, but this, prior to a formal introduction was never a good idea. Mistakes were made.   
Most seem to negotiate this particular/peculiar time of life and end up with a partner to whom a degree of compatibility is possible, even if it be, just a short time. 
Recently, a blog post went viral. It contained advice to good Christian men concerning the qualities and criteria required in a potential wife. It was entitled: ‘Men prefer debt free virgins without tattoos’ and you can access it here. As I recall here are the main exhortations in no particular order. As is my wont, I have added my own incomparable commentary. Their shit in Itallics, my shit, not.
‘Girls, don’t go to college as you will be left/bereft with a legacy of debt and hence men will be reluctant to take you on with the inherited financial liability’. What the author is really concerned about relates to the observation that educated women tend to be independent, opinionated and not willing to be subservient to the will of men. Also, a college education encourages intellectual questioning and rigour and these attributes do not sit well with the unquestioning obedience to Christian dogma. Here is a direct quote from the article: “The husband will need to take years teaching his wife the correct way to act, think, and live since college taught them every possible way that is wrong.”
‘They miss the experience to cook large meals as college does not foster the skill of cooking’.  In other words, the ‘little woman’ should forget about a career and stay at home slaving in the kitchen for her husband. 
Predictably, the prospective bride should be unsullied from the touch of man. Fundamental Christians generally insist on and emphasise the quality of virginity, in both partners. Good luck with that, say I.
The last exhortation concerns body adornment. Now tattoos come in many shades. Having bitter and mild festooned across a women’s breast suggests a low born chick. A small Swallow on a well-turned ankle, not so much. In Tipton, a girl was considered posh if her self inflicted Indian ink tattoos were spelt correctly. Tattoos, like decoration itself, is a matter of taste. But taste, like many things, is not available to all.   
Here are few observations from the Flaxen Haired One: You really need to read the post in its entirety to bask in its insanity. It reads like a 1950s manual for Middle America. Times have certainly changed, for ill or for the better, I’ll leave my gentle readers to judge. To deny modern influences is an unrealistic appreciation of reality. Stay entrenched in the past at your peril and future happiness.
There is a strain/stain throughout the article insinuating that women are intellectually and morally inferior to men. Women need the guidance and teaching that can only be obtained from a man. Shit, men who adhere to the above principles are destined for a sad lonely, frustrated life/wife. The women they seek are as rare as rocking horse droppings. And what happened to that crazy little thing called ‘love’. Romance need not apply. 
                                             Take it away you great, raving, pooftah.

Friday, 20 July 2018

More Liberal Bollocks

More madness from the so-called ‘Liberal Left’. Students at Manchester University have removed Rudyard Kipling’s poem ‘IF’ from a wall and replaced it with a poem entitled, ‘Still I Rise’, by Maya Angelou. 
Of course, when I mean students, I'm not talking about the majority of the student body but a few students who in their wisdom and arrogance have decided what the student body as a whole should view. If you are unfamiliar with the poem, IF, I suggest you visit a previous post of mine concerning the author. To be honest, I’m not a fan of Rudyard Kipling’s work, especially his poetry. However, I can admire the man’s talent, which is undeniable. Therefore, tis is a matter of taste, which is not absolute or easy to pin down. That said, what right have the ‘strident few’ to act as the arbiters of taste for all? In their own words: Today, as a team we removed an imperialist's work from the walls of our union and replaced them with the words of Maya Angelou- God knows black and brown voices have been written out of history enough, and it's time we try to reverse that, at the very least in our union.” [Fatima Abid, the general secretary of Manchester's SU].

How nice for a few ‘right on’ liberals to censor material for the students in general. Heaven forbid that students should think and decide for themselves. And there was me a thinking that higher education is a time to develop critical, independent thought unfettered by irrational bias and coercion.  More fool me. 
Rudyard Kipling is an important British writer and poet. His work should be appraised and read in its historic, contextual setting. Criticise the work on intrinsic artistic merit, but don’t deny people the right to access his work. This is a predictable tactic by the radical Left concerning anything of which they disagree: close it down, deny platform and effectively stifle debate. In a society that considers itself FREE, this is anathema and tantamount to Liberal Fascism and cultural vandalism.
As for the replacement poem, ‘Still I Rise', go read for yourself. However, in my opinion, the poem is shit and the authoress, woefully untalented. But on a positive note, she is black. ARSE.   


Tuesday, 17 July 2018

Ark Encounter

Ken Ham is an Australian living in the US. Nothing remarkable about that. However, Mr Ham is a prominent, vocal, nay strident, proponent of ‘Creationism’ and consequently is not a fan of evolution notwithstanding the overwhelming evidence for the theory. If it contradicts sacred scripture then it can’t be true. Ham and folk of his ilk are happy to bury their intellect in the sand and are not swayed by cogent argument and inconvenient facts which thrust and probe against their irrational but cherished beliefs.

Ham is also the founder of the ‘Ark Encounter’, a theme park for fundamentalist beliefs. Ham, together with his fundy brethren, earnestly believe that the Earth is only 6,000 years old. There is absolutely no evidence to support this viewpoint and indeed there is overwhelming evidence, from numerous sources, to support a 4.5 billion-year-old Earth. Consider how the Colorado River could have carved out the Grand Canyon in 6,000 years. Of course, the rational response is that it has taken millions, perhaps billions, of years to erode the deep gouge in the Earth’s crust. Ham and his cronies are not impressed and are ready and willing to come up with a preposterous counter.

The ‘Ark Encounter’ is a lavish venture, sprawling across acres and nestling cosily to the Kentucky town of Williamstown. An enterprise that only faith and $100,000,000 could spawn. The Ark has been crafted according to biblical proportions and spans a whopping 200 metres in length and comprises seven stories. Modern technology, together with 1000s of artisans crafted the landlocked ship in a mere 2 years. How Noah and his sons constructed the original Ark in 60 years with stone and wooden tools is a conundrum not worthy of rational speculation.

Ham has installed stalls, for two of each kind. Considering the numerous species and their wide-flung geographical distribution it must have taken a miracle to enable all the critters to come together and dutifully enter the Ark without fuss. And then during the voyage, the animals would require fodder and fresh water. Luckily, all creatures of the time were vegetarians so Noah didn’t have to worry about the Velociraptors porking their way through the denizens not equipped with rending talons. I suspect the cleaning of the stalls and the removal of ordure must have been an absolute delight and truly a labour of Job.          

It seems the Ark attraction is not attractive enough and attendance figures are well below the projected expectation of 2 million a year. The economically ailing town of Williamstown has not profited much from the ‘trickle down’ effect either. Predictably, Ham has blamed secularists and atheists for the park’s lacklustre performance, declaring that negative reviews and comments have adversely affected investor confidence. The alternative explanation that perhaps folk can see through the shoddy ‘science’ and the blatant commercialism of the project is not an option for Ham’s contemplation.

Let me be brutal. The ‘Ark Encounter’ is a pernicious monstrosity with an inflated $40 ahead entrance fee. Ham would like young minds to consider the book of Genesis as a factual account dictated by the mind of God. To do so is to contradict almost all that we know about science and the world we live in. He doesn’t want visitors to critically review the theme park’s message, he wants them to accept the whole bizarre story without question. Ham considers himself an educator and an imparter of true knowledge. But he is no educator but a promulgator of extreme religious views at total odds with modern scholarship. Most thoughtful, educated Christians are embarrassed by his primitive strident ramblings and are aghast at a literal rendering of the Old Testament. In the long term, Ham’s Ark may be his undoing. The whole attraction is so blatantly ridiculous that young and increasingly secular Americans will see through the lies and risible fa├žade and make up their own minds. I could be wrong, of course, but I’m an optimist at heart.   

If you really must...........

Wednesday, 11 July 2018

Horizontal Genetic Transfer

When we think of genetic transfer in organisms we think of direct transfer from parents to offspring. But this is not the whole story. For billions of years genes have been transferred between species by a mechanism known as ‘horizontal transfer’. In essence, genes transported this way can become active in the host organism, therefore, contributing to the creature’s metabolism and perhaps ultimately contributing to the evolution of the species. Bacteria are particularly adept at harnessing this mechanism for its own good through the process of conjugation. Genes involved in antibiotic resistance are often transferred this way between bacteria, not necessarily from the same species.

Now you may ask how can this be? How is it possible for genes to be transferred this way? Even genes from plants have been identified in higher animals such as mammals. Although there are several mechanisms involved, retroviruses remain the main vector. As a digression, it is debatable whether viruses can be counted as life. They are comprised of a protein coat enveloping a piece of genetic code and that is basically it. They do not metabolise or grow or exhibit the main characteristics which distinguish life from non-life and yet they are highly successful and ubiquitous, infecting virtually every organism on the planet. I’m inclined to consider viruses as life, but not as we know it. Unfortunately, I don’t have space here to put forth my reasoning and Dioclese castigates me for being too wordy. Arse. Digression endeth.  

Retroviruses have the endearing habit of interlinking their DNA with that of their host. Once the viral DNA leaves during replication it may take chunks of the host DNA with it, thus, the virus particle is able to transfer DNA and genes between members of the same species and between species.

Mosquitos and other blood sustained insects can also act as agents of gene transfer as their blood meal contains DNA from the host. When the insect imbibes again, some of that DNA can be injected into the new host. How foreign DNA integrates into the new host is not well understood but science has shown that it does occur. As mosquitos can feed on different mammalian species this route acts as an important device for horizontal gene transfer.

Various vectors can be utilised by scientists for the process of controlled genetic modification especially involving domestic plant and animal species. In this way, genes which confer positive attributes can be placed into crop and animal genomes. People often have a negative knee-jerk reaction when it comes to genetic modification. However, it should be kept in mind that nature has been transferring genes between species for aeons.    

Humans are not immune from horizontal gene transfer and at least 150 foreign genes have been shown to be intercalated into the human genome including genes from fungi and plants. Foreign genes can undergo regulation by the host genome thus becoming functional. This is not necessarily a positive process. The mechanism is uncomprehending and uncontrolled and is as likely to introduce deleterious genes as well as genes exerting a positive influence. Indeed, several cancer-causing genes (oncogenes) have been found to have originated from other species. Ain’t dat the sad truth.

Hippies, please take note: next time you decide to hug a tree you may actually be snuggling up to a relative- please be gentle. 

I'm a biologist that doesn't like trees- they stare so

Saturday, 7 July 2018

Wakey Wakey

                             I am not a morning person

Over the past 40 years, I have dutifully risen at 6.30am every morning for work. However, I've never really adjusted to functioning at this time in the morning. Everything had to be set up and organised the night before. Clothes laid out, sandwiches made, and car keys exactly in the same place. Every morning consisted of a stumbling, shambling gait, in the semi-dark, as I entertained an imperfect error prone ritual. Sandwiches would be forgotten, and on several occasions odd shoes worn. The odd shoe scenario caused much mirth amongst my colleagues, although it was recognised as part and parcel of my many quirks. Civility and civilisation would only occur after my second cup of strong coffee.

Since retirement I've been suiting myself and rarely rise before 10.00am and to be honest I feel much better for the new regime. I'm not a night Owl either and generally, I'm tucked in and ready for sleep for about 10.00pm. This retirement thingy is certainly to be recommended, tis a wonder I didn't retire years ago. Perhaps the prospect of starving to death was too much to bear?