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PCR and eccentric genius who invented it

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By Prof Kirthi Tennakone
(Email: ktenna@yahoo.co.uk )

Hardly a day passes without the letters, PCR, – the acronym for polymerase chain reaction — being mentioned. To most of us PCR sounds just a test for knowing whether someone has contracted COVID-19 or not.

The polymerase chain reaction is a game changing technique offering diverse and far reaching applications beyond a gold standard for COVID-19 detection.

It is fascinating and entertaining to learn about polymerase chain reaction and its discoverer Kary Mullis, nicknamed untamed genius.

The invention of PCR is intimately connected to our understanding of the cause of biological inheritance. The reason why we have features resembling our parents. A mystery that lead to the discovery of DNA and development of the science of life thereafter. Brief digression into this subject helps to fathom what PCR really means.

Understanding the cause of biological

inheritance and discovery of DNA

Humans have wondered why progeny resemble parents and have some physical and mental traits of the latter. A sprout from a minuscule banyan seed always grows into a gigantus of the same kind but never a tender mustard plant. The ancient Greeks believed that a creature to be born or a plant to germinate subsisted inside the sperm and the seed respectively in their miniature forms. A different idea gained ground later and lasted for more than 2,000 years that physical traits acquired by parents indirectly pass to the offspring. A proponent of this hypothesis in recent times was the French naturalist Lamarck. If Lamarckism were true, amputation of the tails of successive offspring of mice would eventually lead to a generation of tailless rodents. All such experiments failed.

Lamarckism did not confront creationism and intelligent design to the hurt religious establishment. It attracted communists as a way of improving the society to meet ideological aspirations and enhance crop production. The infamous agronomist Lysenko mistrusting proven science attempted to reform Soviet agriculture believing Lamarckian ideals. He probably faked experimental results to justify his thesis and advised famers to abandon use of fertilizers and grow of each crop intensely segregated in order to increase the yield. The result was a famine that starved millions – a good lesson for those who advocate pseudoscience promoting quackeries as remedies for COVID-19 or recommend withdrawal of fertilizer on basis of unreliable claims.

When the world was deluded by Lamarckism, definitive clues as to what really causes inheritance followed from the seminal works two revolutionaries, Charles Darwin and Gregor Mendel.

Darwin in his presentation of the theory of evolution noted that the decedents of a given species, sometimes include one’s with distinct variations in their characteristics, referred to as mutants. If the new qualities acquired by the mutants fits the environment, they survived and continuation of evolution via natural selection led to the emergence of new species.

Another question crucial to understand the cause of inheritance has been how the traits of male and female sexual partners were represented in the offspring? Without resorting to experiment and careful analysis, the conservative stream of biologists continued to believe it should be a blend of the maternal and paternal traits. In late 1890s, the work of the Austrian monk Gregor Mendel, a mathematician and a botanist as well, provided a conflicting answer. In an experiment lasting for eight years Mendel planted different strains peas, cross-pollinated them and germinated the seeds brought forth to see features of the of linage such as the height to which they grew and the colour of flowers. His results did not indicate blending of traits, instead the original attributes appeared in each generation with different probabilities. Crossing tall and dwarf varieties never procreated medium size plants; instead, they were either tall or dwarf. Mendel concluded that traits were passed to the progeny as distinct qualities – what we refer to as genes today.

The work of Darwin and Mendel compounded by subsequent findings, pinpointed the inescapable conclusion that a chemical substance transmitted inheritance. Many believed it should be a protein. In 1942, the prescient Austrian physicist Erwin Schrodinger, famous for the quantum theory, expressed an alternative opinion. He hypothesized that the heredity determining entity, needed to be a molecule capable of encoding information and replication. Aroused by Schrodinger’s proposition, chemists all over the world competitively researched to identify the causative agent. In early 1950s, American biologist Watson and British physicist Crick, showed that the genetic material found in cells of animals and plants was deoxyribonucleic acid DNA – a lengthy molecule constituted basically of two strands of four different repeated subunits. Molecules of DNA encode information using these units as a four letter alphabet.

Cells of every organism contain DNA characteristic to the species and unique to each individual. The order in which millions of these units sequentially are arranged in a helical chain, is analogous to an instruction manual detailing the development of the organism. Short sequences of the four units in the chain represent genes, dictating special instructions, just like a sentence or a paragraph in the manual.

Polymerase chain reaction (PCR) and its uses

PCR is a technique of amplifying million-fold a tiny quantity of DNA representing a sequence of interest in minutes so that it could be detected even in minutest quantities – justifying the use of the term chain reaction with polymerase as the catalyst ensuing the reaction. In the analogy of DNA to an instruction manual, PCR would be like inserting a book mark to fix a certain page and copying that page many times.

In finest detail DNA is unique to each individual, whether it is a human or a bacterium. The difference between DNAs of individuals in a given species is minuscule. Yet, the identity of a person can be established from DNA in the smear of saliva over a stamp by PCR. Again just like finding a needle in a hay stack, minute quantities of a specific type of DNA in a sample containing excessive quantities of DNAs from background sources, can be selectively ascertained by running a PCR. The technique finds wide range of applications in medical diagnostics, forensics and criminology, archaeology and paleontology, phylogenetics, cloning, gene editing etc.

How is PCR detecting corona virus?

The genetic material of the corona virus is RNA – a single strand of DNA. The test first converts RNA into DNA making it double stranded and then selectively amplify a fragment of DNA covering a specific sequence using special reagents. The amplification enables detection by a screening system. Test is extremely sensitive; in fact, too sensitive, responding to even the dead fragments of the virus.

The impact of PCR on forensics and criminology is unprecedented. The technique has enabled not only identification of criminals but also the exoneration of innocent. A man on death row for eight years has been released and compensated as PCR became available.

Kary Mullis: The man who discovered PCR

Kary Mullis born in Southern United States 1944 was exceptional and radical. As a high schooler he meddled with chemicals at home and created an ingenious technique for making rocket fuels. His homemade rockets propelled miles into the sky frightening pilots maneuvering airplanes to land. Having earned a bachelor’s degree in chemistry from Georgia Institute of Technology he moved to University of California, Berkeley to pursue studies towards a doctoral degree in chemistry. A fashionable field of study at that time was chemistry of DNA or molecular biology. Instead of following courses in biochemistry needed for the thesis, he opted for astrophysics, saying he could learn the former discipline talking to colleagues. He wrote an article on a fundamental problem in astrophysics and succeeded getting it printed in the prestigious journal Nature. He was a surfing enthusiast and guitarist.

At the oral examination for qualifying to register as a doctoral candidate, Mullis was found to be unprepared and weak in conventional biochemistry. However, his paper on an astrophysical subject rather than biochemistry saved him from disqualification. The committee decided despite odd behaviour and unpreparedness, the man was talented and granted him approval for registration. Mullis earned a Ph.D. in 1973 and decided to give up research to become a writer and worked in a restaurant. Later, one of his friends persuaded him to a job in a biochemical company, at least to earn a living. There, he worked in a laboratory devoted to DNA chemistry, often quarrelling with coworkers. In early 1980s, he came up with the idea of PCR, but no one took him seriously. The paper he wrote was rejected twice and finally published in a less acclaimed journal. Soon the world acknowledged the utmost significance of his work and Mullis shared 1993 chemistry Nobel Prize. He resorted to eccentric behaviour criticizing the establishment and mainstream thinking, earning reputation as the untamed genius. When he was invited to a high-standing conference on molecular biology, he projected three slides of female nudes, lambasted the way of funding research and vanished! In an interview, Mullis has said Nobel Prize serves as a licence to do things unacceptable.

Kary Mullis, who passed away in 2019, will be remembered as a demarcater of biology into two epochs – before PCR and after PCR. Fortunately, the pandemic is post – PCR. Otherwise the situation would have taken a more deadly and devastating turn.

The invention of PCR stands as a prime example to highlight how fundamental studies motivating creativity, foresight and hard work can pay off unexpectedly. A constant reminder to research and academic institutions to retain this spirit of accommodating the most talented and not the mediocre who entertain trivialities for the shake of survival. The latter even amend (adulterate) the established mandates for fostering advanced studies to suit them. And deceiving the policymaker and general public, stating the amendments (adulterations) were affected to meet national interest (self-interest).

Would a man of the calibre of Kary Mullis be considered for employment or allowed to continue in our institutions? Will a committee here act with the same altruism and consideration as the one that endorsed the candidature of Kary Mullis?



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Features

Terror figuring increasingly in Russian invasion of Ukraine

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In yet another mind-numbing manifestation of the sheer savagery marking the Russian invasion of Ukraine, a shopping mall in Ukraine’s eastern city of Kremenchuk was razed to the ground recently in a Russian missile strike. Reportedly more than a hundred civilian lives were lost in the chilling attack.

If the unconscionable killing of civilians is a definition of terrorism, then the above attack is unalloyed terrorism and should be forthrightly condemned by all sections that consider themselves civilized. Will these sections condemn this most recent instance of blood-curdling barbarism by the Putin regime in the Ukrainian theatre and thereby provide proof that the collective moral conscience of the world continues to tick? Could progressive opinion be reassured on this score without further delay or prevarication?

These issues need to be addressed with the utmost urgency by the world community. May be, the UN General Assembly could meet in emergency session for the purpose and speak out loud and clear in one voice against such wanton brutality by the Putin regime which seems to be spilling the blood of Ukrainian civilians as a matter of habit. The majority of UNGA members did well to condemn the Russian invasion of Ukraine close on the heels of it occurring a few months back but the Putin regime seems to be continuing the civilian bloodletting in Ukraine with a degree of impunity that signals to the international community that the latter could no longer remain passive in the face of the aggravating tragedy in Ukraine.

The deafening silence, on this question, on the part of those sections the world over that very rightly condemn terror, from whichever quarter it may emanate, is itself most intriguing. There cannot be double standards on this problem. If the claiming of the lives of civilians by militant organizations fighting governments is terror, so are the Putin regime’s targeted actions in Ukraine which result in the wanton spilling of civilian blood. The international community needs to break free of its inner paralysis.

While most Western democracies are bound to decry the Russian-inspired atrocities in Ukraine, more or less unambiguously, the same does not go for the remaining democracies of the South. Increasing economic pressures, stemming from high energy and oil prices in particular, are likely to render them tongue-tied.

Such is the case with Sri Lanka, today reduced to absolute beggary. These states could be expected ‘to look the other way’, lest they be penalized on the economic front by Russia. One wonders what those quarters in Sri Lanka that have been projecting themselves as ‘progressives’ over the years have to say to the increasing atrocities against civilians in Ukraine. Aren’t these excesses instances of state terror that call for condemnation?

However, ignoring the Putin regime’s terror acts is tantamount to condoning them. Among other things, the failure on the part of the world community to condemn the Putin government’s commissioning of war crimes sends out the message that the international community is gladly accommodative of these violations of International Law. An eventual result from such international complacency could be the further aggravation of world disorder and lawlessness.

The Putin regime’s latest civilian atrocities in Ukraine are being seen by the Western media in particular as the Russian strongman’s answer to the further closing of ranks among the G7 states to the Russian invasion of Ukraine and the issues growing out of it. There is a considerable amount of truth in this position but the brazen unleashing of civilian atrocities by the Russian state also points to mounting impatience on the part of the latter for more positive results from its invasion.

Right now, the invasion could be described as having reached a stalemate for Russia. Having been beaten back by the robust and spirited Ukrainian resistance in Kyiv, the Russian forces are directing their fire power at present on Eastern Ukraine. Their intentions have narrowed down to carving out the Donbas region from the rest of Ukraine; the aim being to establish the region as a Russian sphere of influence and buffer state against perceived NATO encirclement.

On the other hand, having failed to the break the back thus far of the Ukraine resistance the Putin regime seems to be intent on demoralizing the resistance by targeting Ukraine civilians and their cities. Right now, most of Eastern Ukraine has been reduced to rubble. The regime’s broad strategy seems to be to capture the region by bombing it out. This strategy was tried out by Western imperialist powers, such as the US and France, in South East Asia some decades back, quite unsuccessfully.

However, by targeting civilians the Putin regime seems to be also banking on the US and its allies committing what could come to be seen as indiscretions, such as, getting more fully militarily and physically involved in the conflict.

To be sure, Russia’s rulers know quite well that it cannot afford to get into a full-blown armed conflict with the West and it also knows that the West would doing its uttermost to avoid an international armed confrontation of this kind that could lead to a Third World War. Both sides could be banked on to be cautious about creating concrete conditions that could lead to another Europe-wide armed conflict, considering its wide-ranging dire consequences.

However, by grossly violating the norms and laws of war in Ukraine Russia could tempt the West into putting more and more of its financial and material resources into strengthening the military capability of the Ukraine resistance and thereby weaken its economies through excessive military expenditure.

That is, the Western military-industrial complex would be further bolstered at the expense of the relevant civilian publics, who would be deprived of much needed welfare expenditure. This is a prospect no Western government could afford to countenance at the present juncture when the West too is beginning to weaken in economic terms. Discontented publics, growing out of shrinking welfare budgets, could only aggravate the worries of Western governments.

Accordingly, Putin’s game plan could very well be to subject the West to a ‘slow death’ through his merciless onslaught on the Ukraine. At the time of writing US President Joe Biden is emphatic about the need for united and firm ‘Transatlantic’ security in the face of the Russian invasion but it is open to question whether Western military muscle could be consistently bolstered amid rising, wide-ranging economic pressures.

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At 80, now serving humanity

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Thaku Chugani! Does this name ring a bell! It should, for those who are familiar with the local music scene, decades ago.

Thaku, in fact, was involved with the original group X-Periments, as a vocalist.

No, he is not making a comeback to the music scene!

At 80, when Engelbert and Tom Jones are still active, catering to their fans, Thaku is doing it differently. He is now serving humanity.

Says Thaku: “During my tenure as Lion District Governor 2006/2007, Dr Mosun Faderin and I visited the poor of the poorest blind school in Ijebu Ode Ogun state, in Nigeria.

“During our visit, a small boy touched me and called me a white man. I was astonished! How could a blind boy know the colour of my skin? I was then informed that he is cornea blind and his vision could be restored if a cornea could be sourced for him. This was the first time in my life that I heard of a cornea transplant. “

And that incident was the beginning of Thaku’s humanity service – the search to source for corneas to restore the vision of the cornea blind.

It was in 2007, when Dr Mosun and Thaku requested Past International President Lion Rohit Mehta, who was the Chief Guest at MD 404 Nigeria Lions convention, at Illorin, in Nigeria, to assist them in sourcing for corneas as Nigeria was facing a great challenge in getting any eye donation, even though there was an established eye bank.

“We did explain our problems and reasons of not being able to harvest corneas and Lion Rohit Metha promised to look into our plea and assured us that he will try his utmost best to assist in sourcing for corneas.”

Nigeria, at that period of time, had a wait list of over 70 cornea blind children and young adults.

“As assured by PIP Lion Rohit Mehta, we got an email from Gautam Mazumdar, and Dr. Dilip Shah, of Ahmedabad, in India, inviting us for World Blind Day

“Our trip was very fruitful as it was World Blind Day and we had to speak on the blind in Nigeria.”

“We were invited by Gautam Mazumdar to visit his eye bank and he explained the whole process of eye banking.

“We requested for corneas and also informed him about our difficulties in harvesting corneas.

“After a long deliberation, he finally agreed to give us six corneas. It was a historical moment as we were going to restore vision of six cornea blind children. To me, it was a great experience as I was privileged to witness cornea transplant in my life and what a moment it was for these children, when their vision was restored.

“Thus began my journey of sight restoration of the cornea blind, and today I have sourced over 1000 corneas and restored vision of the cornea blind in Nigeria, Kenya and India till date.

“Also, I need to mention that this includes corneas to the armed forces, and their family, all over India.

“On the 12th, August, 2018, the Eye Bank, I work with, had Launched Pre-Cut Corneas, which means with one pair of eyes, donated, four Cornea Blind persons sight will be restored.”

Thaku Chugani, who is based in India, says he is now able to get corneas regularly, but, initially, had to carry them personally – facing huge costs as well as international travel difficulties, etc.

However, he says he is so happy that his humanitarian mission has been a huge success.

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Health services face imminent collapse due to fuel crisis

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A file picture of a recent doctors’ protest

By Dr B. J. C. PERERA

MBBS(Cey), DCH(Cey), DCH(Eng), MD(Paed), MRCP(UK), FRCP(Edin), FRCP(Lon), FRCPCH(UK), FSLCPaed, FCCP, Hony FRCPCH(UK), Hony. FCGP(SL)

Specialist Consultant Pediatrician and Honorary Senior Fellow, Postgraduate Institute of Medicine, University of Colombo, Sri Lanka.

Our free National Health Service is something that brings succor to the poorest of the poor, as well as even the well-to-do, and everybody in-between. As a country and a nation, we are so proud of our health services. In fact, as a developing country, we have shown the entire world how much can be accomplished, even with our meager resources, and with so few facilities made available to us in our health facilities. Our healthcare personnel are second to none anywhere else on the planet, and they try to do their best, even under trying circumstances.

There are shortages of medicines, disposable articles and equipment in our healthcare institutions. It has really gotten worse during the current economic crisis. Yet, we have managed to rise above all that, innovate, beg, borrow and do our best for the patients who come to us. Generally, our health workers will not allow a life to be lost without a fight. A case in point is how these personnel, from the lowest-ranked to the highest, rose and fought tooth and nail during the current COVID-19 pandemic. They worked without any worthwhile rest, even foregoing their meals when things had to be done to save lives. Our countrymen and countrywomen hailed us as their saviours, singing hosannas to all of them for so selflessly handling the crisis. The healthcare personnel showed results and they sacrificed many things and went through hell on earth, to save lives.

However, there is a looming dragon that is likely to inflict telling blows to cripple this hallowed service that is provided for our people. It is not due to shortages of drugs or equipment. Those can be handled to the very best of our abilities. The problem is due to severe human resource depletion that is the likely result of the current fuel shortage. It is a looming catastrophe, as large as life, where our healthcare personnel will not be able to get to their places of work, and they will not be able to respond to sudden emergencies, as there is no transport. The government, ministers and all other stupid politicians do not seem to realise this, and perhaps could not even care less about that. That is of course to be expected, as they have their agendas. They will somehow get their things done, but the people who suffer would be the poor who come to our hospitals.

However, the most distressing thing about this entire fiasco is how among our general public, the thugs, ruffians, desperados, those engaged in nefarious hoarding of fuel and all kinds of Mafias, are beginning to treat healthcare personnel at fuel queues and fuel sheds. Healthcare personnel are not asking for special treatment at fuel stations. They are an absolutely essential service, and all they are asking is for some fuel to enable them to attend to their essential service provisions. Even ambulances have to wait in queues, and are not allowed by the irate public to get priority for fuel.

A couple of weeks ago we saw in the news that a lady doctor driver was driven away from a fuel station by a mob. The most distressing thing about that entire episode was the bravado of a non-health staff lady driver, who shouted with powerful gesticulation of her arms that she had children in the car and could not make concessions to lady doctors. God forbid, but what if one of those children suddenly fell ill and the person to attend to them was the very same lady doctor who was chased away, and that person was not able to get to the hospital due to the lack of fuel?

Starting from Friday the 24th of June 2022, there was a lukewarm arrangement made to provide fuel to essential services, from certain designated fuel stations. every Friday. This was not communicated properly through all the media, and in very many places the public vehemently objected to this. The Borella junction Ceypetco fuel shed was one of the stations which were allocated for this purpose, where the essential services people, including healthcare personnel, queued up in their vehicles from around 6.00 am. The bowsers of fuel arrived only in the late evening, after a 12-hour long wait. There was hardly any security cover and virtually a free for all, with the sparse security personnel turning a blind eye to all the misdemeanors of the general public. There were loads of nurses, doctors and other healthcare workers from the National Hospital, Lady Ridgeway Hospital for Children, National Eye Hospital, De Soysa Maternity Hospital and the Castle Street Hospital for Women, who were in these vehicle queues, twiddling their thumbs and being forced to keep away from their places of work. No doubt, these hospitals worked with only minimal skeleton staff. All these hospitals have a collective staff strength running into very large numbers, all working in an absolutely vital essential service. In some outstation areas, the incensed public insisted on the healthcare personnel queuing up with the general public, even on that dedicated Friday, and at least in one area, the hospital had to be closed as most of the hospital staff had to be in fuel queues. For whatever it is worth, this writer has not been able to see his patients for more than a week due to lack of fuel.

Unless a proper system to provide fuel to essential services is implemented by this impotent government, this situation will go from bad to worse. Many hospitals will have to be closed, not due to strikes or trade union actions, but due to a lack of human resources to run the hospitals. Medical personnel will not be able to attend to emergencies, especially outside working hours, and many lives will be lost. Our inability to provide timely treatment could also lead to some patients being maimed for life.

So be warned, our people of our own country. Selfishness and scant regard for law and order on the part of the general public will lead to an unprecedented catastrophe. There will be riots inside and outside the medical institutions with damage to public property. Innocent lives will be lost and blood will necessarily have to be on the hands of the decision-makers and the powers-that-be.

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