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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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Trump Walks Out of the White House Into A Minefield of Legal Perils!

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WHAT DONALD IS NOW UP AGAINST . . .

by Selvam Canagaratna

“Nobody has a more sacred

obligation to obey the law than those who make the law.”

Jean Anouilh, Antigone, 1942.

“At some point in the next few weeks, Donald Trump will face his second Senate trial following an impeachment by the House of Representatives. Unlike the proceedings in late 2019 and early 2020, this time around — in the wake of the attempted coup on January 6th carried out by a violent mob inspired by Trump’s words to attack the US Congress — the process has been swift,” wrote Sasha Abramsky, a freelance journalist and a part-time lecturer at the University of California at Davis, in Truthout magazine.

The House impeached Donald Trump after a debate that lasted a mere few hours.

Given Trump’s inflammatory words on January 6th, and the unwillingness of senior lawyers to rally to his defense, and given the fact that has now publicly laid blame for the violent events squarely on Trump’s shoulders, the disgraced ex-President’s trial in the Senate could be almost as rapid.

If there is any honour whatsoever among GOP senators — or for that matter, any ability to think long-term about their own political self-interest — he will become the first President in US history to be convicted by that body. Of course, since he will have already left office, he won’t, alas, become the first President to be removed from power via an impeachment and trial process.

That’s a shame, but it doesn’t make the process any less vital. If American democracy is to survive, if political decisions aren’t to be held hostage by gun-wielding fanatics, Trump’s effort to undermine the peaceful transfer of power following an election must face real consequences.

Conventional wisdom has it, however, that most GOP senators, no matter how personally distasteful they find Trump and how terrified they were by his unleashing of a mob against them on January 6th, won’t want to antagonize their base by voting to convict. Conventional wisdom has it that, when push comes to shove, appeasement will win the day.

But in this instance, might conventional wisdom be wrong? As Mitch McConnell seems now to have concluded, and as and many of his caucus likely soon will, having shamefully enabled Trump these past four years, they now have precious little incentive to waste political capital on a wounded and discredited ex-President, a man who has lost his hold on many independents as well as on a significant minority of GOP voters.

To the contrary, they have every incentive, as more and more evidence of his malfeasance surfaces, to utterly disempower this demagogue in order to ensure that he can’t rise from the political ashes to wreak vengeance on those in the GOP who didn’t help him in his coup attempts. Convict him, and they can then, in quick order, pass legislation barring him from ever running for public office again — a fate that, surely, no public figure in American history has so richly deserved, and one that must have McConnell and other GOP leadership figures in the Senate privately salivating in delight. True, this would alienate a not insignificant proportion of the GOP base; but in the long run that might well be less damaging than alienating the independents who are so central to creating a viable electoral coalition for both political parties.

Were the Senate to turn on Trump in this way, McConnell would risk fracturing his base; after all, , and only coup. But if McConnell and the GOP establishment don’t seize this particular bull by its horns they risk being reduced to an extremist party incapable of attracting anyone outside of their shrinking base. In the long run, backing the conviction of Trump might offer them a one-off chance to cauterize their party’s bleeding wound, and to sever its joined-at-the-hip connection to an authoritarian leader who stoked a mob bent on assassinating elected officials. This is a phrase I never thought I’d write, but… “If I were Mitch McConnell, I’d seize the moment and throw Trump as far under the bus as I could possibly manage.”

For here’s the thing: If McConnell doesn’t lend his support — and, by extension, many of the other GOP senators’ support — to conviction, it will only further erode GOP credibility among the broader electorate if, over the coming months, as seems increasingly likely, Trump is indicted in a number of state courts for his myriad crimes. The lower Trump’s legal fortunes sink, the worse the senate will look if it twice exonerated him for his actions despite a preponderance of evidence indicating his guilt.

How would voters react if McConnell, after acknowledging Trump’s culpability for triggering the attempted coup, then pushed to give the man a free pass for it, only to have Georgia show more spine by indicting him for threatening a public official and demanding votes “be found” to guarantee Trump a victory he hadn’t legitimately won?

How would they react if New York State indicted Trump and miscellaneous family members for tax fraud, or campaign finance law violations, or possibly even money laundering, if some of the allegations surrounding his relationship to Russian mobsters turn out to have substance? How would they react if the for his role in the events of January 6? How would they react if — essentially for pimping out his services to foreign governments and entities?

when he leaves office on Wednesday. But, in addition, he is facing a number of as well, including from women who allege he assaulted them in the years before he became President. Given the events of the past two weeks, he may well also face numerous other civil lawsuits, including damages claims from family members of the victims of the January 6 Capitol breach. In each of these trials, evidence will be presented — and the public will see and read that evidence — that will make Trump look more awful by the minute. The further out we get from the Trump era, chances are, the more clear the harm he inflicted will become.

Trump’s corporate backers realize this. Belatedly, he is being cut off from his go-to financing sources, including Deutsche Bank, which has said it will no longer do business with him. As a result, as his legal woes mount, he will likely have to resort to crowd-sourced, dodgy money-making schemes simply to get his gullible supporters to pony up cash to fund his defense attorneys.

Although the fates may have finally caught up with this grifter, the political firestorm he helped create remains. For as Trump leaves the White House, his far-right supporters won’t magically disappear. Trumpism and its toxic spin-offs — from QAnon to the Proud Boys — will remain a threat on the American political landscape for years to come. That, alas, is the sobering reality as a new presidency gets underway and as Donald Trump, from domestic exile in Mar-a-Lago, prepares for his second Senate trial.

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Jagan in R. K. Narayan’s “Vendor of Sweets”

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The world- renowned author R.K Narayan’s novel “Vendor of Sweets” is undoubtedly a worthy contribution to the world of English literature. Born in Madras in 1906, Narayan hailed from an entirely orthodox family. This traditional up-bringing may have influenced him in presenting Jagan’s character in the story.

The story set in the post-independent era in India revolves round, as the title suggests, a vendor of sweets. Narrated in the medium of a third person Narayan uses the English language very effectively to portray characters which are essentially Indian. Yet the reader’s response is rather intimate as the characters transcend time, culture, geographical boundaries, religion etc. thereby achieving universality. In the ensuing analysis let us see how Narayan sketches Jagan’s character to achieve this universality.

As the story begins, we meet Jagan, the vendor of sweets in conversation with his cousin whom the narrator says that no explanation could be given as to how he came to be called so.

The first glance at Jagan gives an insight into his character when he says “conquer taste and you will have conquered the self” This extract from the Holy Scriptures quoted by Jagan was questioned by the cousin, “Why conquer self?” Jagan’s reply was “I do not know, but all our sages advise us so.” This is Jagan who Narayan portrays. The lack of analytical sense is him made him what he was.

This trait in him develops further as the story wends its way towards that tragic end. His limited capacity into in-depth thinking prompted him to accept whatever the sages say. He is unable to give an explanation as to why the taste should be conquered. He accepts it merely because the sages say so. This feature in him prevented his independent thinking. The cousin’s character in contrast with his inquiring mind sheds light on the portrayal of Jagan’s.

We see this trait extending further in his life in most of his dealings. For example, we know that he was in the forefront of the Indian Independence struggle ardently following Gandhi in his nonviolence campaign. What is striking is the fact that he followed Gandhi’s nonviolence policies to the letter and went to the extent of making his shoes out of the skin of an animal which had died due to old age. His words quite rightly justify the point. “I do not like to think that a living creature should have its throat cut for the comfort of my feet”

It is this behavior that makes us think of him as an extremist. He ventures into extremes without being realistic. His attitudes towards his wife’s sickness is one such instance where he became tenacious in the belief that only indigenous medicine can cure her headache. The narration stands to show that their first clash cropped up over such an argument.

The absence of an analytical mind drove him towards diffidence. He lagged behind taking decisions of his own. Even in the transactions with his son he needed cousin’s help to communicate. When his son told him that he wanted to give up his studies in College, he was aghast. His expectations of his son were entirely different. He wanted his son to pursue his studies and collect a BA degree. But he lacked confidence to discuss the matter with the son. He sought cousin’s help to mediate with the son. The cousin’s advice was that it would be best to know from the boy himself. He even suggested “why don’t you have a talk with him?” Jagan responded “Why don’t you?” This is a clear indication of Jagan’s character as a man who is not strong enough to take up challenges.

The home environment was such that the communication between father and son had come almost to a stand-still in the aftermath of the mother’s death. Jagan played the maternal role of feeding the boy properly but he paid little or no attention to the boy’s mental well-being. He was proud that Mali had grown physically. The narration stands to show that he was very proud of his son’s height, weight and growth. But he neglected the fact that as he grows his needs, requirements and aspirations need to be soothed for the wellbeing of his mental growth. He forgot the fact that his son is growing up without the warmth of the mother.

Jagan was in the habit of reading the “Bhagavad Gita” even in the midst of his business activities. However, his concentration on the religious scriptures was invariably hindered with the slightest quietening of the sizzling in the kitchen or if he noticed any slackness at the front stall. If a beggar is spotted by him near the entrance, he would shout “Captain, that beggar should not be seen here except on Fridays. This is not a charity house.” Such acts of Jagan revealed in no uncertain terms his hypocrisy and we know that his hypocritical demeanour was seen in many of his dealings.

Besides, Jagan was somewhat displeased when the trays in the sweet shop returned with the left-overs. It bothered him as if he had a splinter in his skull. When the head cook suggested that they can be turned into a new sweet for the next day, forgetting all his holy scriptures he readily agreed to it, saying “After all everything consists of rice, flour, sugar and flavours…..” His lofty ideals were mere lip-service and clear manifestation of hypocrisy in Jagan.

His hypocrisy does not end at this point. It further extends. We know that he maintained two books to record his business accounts. Narayan, very sarcastically records this act of Jagan when he puts it, “…… arising out of itself and entitled to survive without reference to any tax.” Such acts of dishonesty clashed with his so-called religious principles and the reader responds with discreet sarcasm.

A character sketch of Jagan is incomplete if no mention is made about his inter-personal skills. As mentioned above, his relationship with his wife and son ended in failure and so was his relationship with the members of the extended family. The narration reveals Jagan reflecting “They never liked me” and further the narrator’s words “Thus he had escaped the marriages of his nieces, the birthdays of his brother’s successive children and several funerals” What we gather from the narration is that Jagan felt grateful for being an outcast as it relieved him from his family obligations. This feature in Jagan drives home the point that Jagan was a failure in maintaining inter-personal skills which ultimately made his life pathetic.

This is Jagan we meet in Narayan’s “Vendor of Sweets” In Jagan we see a man not put into a frame. A blend of good and bad. A person made of flesh and blood and we begin to wonder whether we have not met him somewhere, in our daily transactions. Jagan is a victim not of evil but a victim of his own silly, weak or strange but harmless aspects of character. Jagan is essentially Indian but his hopes, aspirations and dreams are universal.

 

Written by Vivette Ginige Silva

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R.K. Lionel Karunasena, fine athlete and exemplary police officer

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Twenty years ago Lionel Karunasena had a heart attack while taking his constitutional walk at the Bambalapitiya Police park and collapsed.

He was born on January 2, 1945, in Ratnapura. He studied at the Seevali Maha Vidyalaya, Ratnapura, excelling not only in his studies but also in athletics. His forte was long jump and the triple jump. He was spotted by the talent scouts of the Ceylon Track and Field Club (CT &FC) and enrolled him to the club and found employment at Air Ceylon.

On November 11, 1964 at the CT& FC- University Athletics dual meet, he equaled the national long jump record of 24 feet two and a half inches established by N.A Weeratunga of the Mercantile AAA on the December 28, 1956.

The writer was a witness of this event. In his allotted six attempts, he jumped over 22 ft. One jump was nearly 25 feet but he over stepped the board. In his fourth jump he leapt into fame equaling the Ceylon record. This record was broken only in 1985!

At the Ceylon 1964 AAA nationals, he was placed third in the long jumps event. He won the event in 1965 and 66. His ambition in life was to serve as a protector of law and order. In order to achieve this, he joined the police as a sub inspector on June 26, 1967.

Despite his busy schedule as a police officer he continued to be involved in athletics representing the police. In 1977, he came third at the AAA Nationals when two Indian athletes, P. Bannerjee and Mohinder Singh took first and second places.

He represented Sri Lanka at the Asian Games in 1966 at Bangkok and again at Bangkok in 1970.

In the all-time list computed by the Sri Lanka AAA recorder, Lionel Karunasena ranks second.

He always believed in equality and denounced social injustices. Due to his dedication towards duty he won quick promotions and rose to the rank of DIG. His first appointment as DIG was to the Wanni. Here he was required to be in the war front. There he was a shining example to his colleagues.

He often visited the many camps in the war zone.

He served as the Commanding officer of the Police STF for over 13 years and was the fourth commanding officer of the STF. He had a miraculous escape when President Premadasa was killed by a suicide bomber on May 1, 1993. Seventeen others were killed along with the President.

He was a highly respected office in the police. His wife Chitra, daughter Sarika and son Shalike were well aware that he was a committed officer and at the same time a loving wife and devoted father. His long and dedicated service will be written in gold. May his journey through samsara be short and peaceful.

 

K.L.F.Wijedasa

100,Barnes Place – 7 Colombo

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