By Prof Kirthi Tennakone
(Email: firstname.lastname@example.org )
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?
31st night…Down Under
The NYE scene at the Grand Reception Centre, in Melbourne
Despite the COVID-19 restrictions, the Voluntary Outreach Club (VOC) in Victoria, Australia, was able to hold a successful New Year’s Eve celebration, at The Grand Reception Centre, in Cathies Lane, Wantirna South.
In a venue that comfortably holds 800, the 200 guests (Covid restrictions), spanning three generations, had plenty of room to move around and dance to the array of fabulous music provided by the four bands – Replay 6, Ebony, Cloud 9 with Sonali, Redemption and All About That Brass.
The drinks provided, they say, oiled the rusty feet of the guests, who were able to finally dress up and attend such an event after nine months of lockdown and restrictions. With plenty of room for dancing, the guests had a thoroughly enjoyable time.
According to an insider, the sustenance of an antipasto platter, eastern and western smorgasbord, and the midnight milk rice and katta sambol, were simply delicious, not forgetting the fantastic service provided by Jude de Silva, AJ Senewiratne and The Grand staff.
The icing on the cake, I’m told, was the hugely generous sponsorship of the bands by Bert Ekenaike. This gesture boosted the coffers of the VOC, which helps 80 beneficiaries, in Sri Lanka, comprising singles and couples, by sending Rs. 3,000 to Rs. 3,500, per month, to each of these beneficiaries, and augmenting this sum, twice a year, in July and December, with a bonus of the same amounts.
Strategies for effective management
by Prof. Rohan Rajapakse
Emeritus Professor of Entomology University of Ruhuna and former Executive Director Sri Lanka Council of Agriculture Research Policy
Fall armyworm Spodoptera frugiperda (Lepidoptera; Noctuidae), a quarantine pest, has been identified as a very destructive insect pest of Maize/Corn. This insect originated in Americas and invaded the African region in 2016 and was detected in India the following year and perhaps would have naturally migrated to Sri Lanka last year from India. Now, it is reported that FAW is present in all districts of Sri Lanka except Nuwara-Eliya and Jaffna. In winter in the USA the pest is found in Texas and Florida and subsequent summer when it gets warmed up, the pest migrates up to the Canadian border. The corn belt of China is also at a risk due to its migratory habit and the cost to Africa, due to this invasion, will exceed $ 6 billion. Maize is a staple food crop in Africa and millions depends on it for food. Hence in Africa and now in Asia it is a global food security issue for millions of people that could be at a risk if FAW is not controlled. The adult moth migrates very fast almost 100 km every night and nearly 500 km, before laying 1,500 eggs on average. The entire life cycle lasts 30 days in tropical climate. There are six larval instars and mostly the destruction is caused by the last three instars and the growing moth pupates in the soil for 10-12 days and the nocturnal adults lay eggs on leaves for about 10 days The pest thrives on about 80 host plants but the most preferable host is Corn/Maize. In Sri Lanka the preferred hosts includes Kurakkan and Sugarcane in addition to Maize. The symptoms of damage- scrapping of leaves, pin holes, small to medium elongated holes. Loss of top portion of leaves fecal pellets in leaf whorl which are easily recognizable. The Comb is also attacked in later stages with a heavy infestation, but after removing the FAW affected portion of the comb the remaining portion is still suitable for consumption and there is no fear of any toxicity. There are two morphologically identical strains––maize strain that feeds on maize and sorghum, and rice strain that feeds on rice and pasture grasses. However, in Sri Lanka only the maize strain has been detected so far. FAW thrives in a climate where drought is followed by heavy rains on a similar way we have experienced last year.
Although new agricultural insect pests are found in Sri Lanka, from time to time a number of factors make FAW unique (FAO Publication 2018)
FAW consumes many different crops 2 FAW spreads quickly across large geographical areas 3.FAW can persists throughout the year. Therefore Sri Lanka needs to develop a coordinated evidence based effort to scout FAW for farming communities and effective monitoring by the research staff
Since the pest has already arrived in Sri Lanka, the Government/ Ministry of Agriculture should formulate short, mid and long term strategies for its effective management with all stakeholders. Also it has to be clear that a single strategy ex pesticides will not help in effective control but a proper combination of tactics, such as integrated pest management should be employed in the long term. In the short term, the recommended pesticides by the Department of Agriculture should be employed along with cultural and sanitary control strategies. These strategies have now been formulated and what is required to enlighten the farmers and people by utilizing the trained staff. The country should be placed on a war footing and an emergency should be declared in the affected areas to coordinate the control strategies. The integrated control tactics, such as cultural control, should be integrated with pesticides based on the recommendation of the research staff. The residues should be destroyed after harvest and avoid late planting and staggered planting. The Ministry of Agriculture should create awareness among the farmers and train the farmers on early detection of egg masses found on leaves and destroy them by hand. The pesticides for FAW control is recommended by the Department of Agriculture (Please contact Registrar of Pesticides of the Department of Agriculture for the recommended list of Pesticides) and they have to make it available at subsidized rates or given free with technical information considering the emergency. When the larvae are small early detection and proper timing of pesticides are critical for elimination of the pest. With this outbreak some farmers and the private sector is engaged using highly hazardous pesticides which should be avoided to make way for sustainable alternatives. The Department Entomologists should train the farmers for early detection of egg masses when present on 5% of the plants and when 25% of the plants show damage symptoms and live larvae are present on war footing. The economic threshold has been calculated as 2-3 live larvae per plant and the control strategies should commence as soon as this threshold is detected by visual observation. The majority of development officers, agriculture and science graduates working in Divisional Secretariats, are already trained on pest control and their participation on training the farmers for early detection and pesticide selection and application warrants the strategy. Some of the recommended pesticides are follows: Chlorantraniliprole 200g/1SC: Trade name Corogen, Emamectin benzoate 5%SG: Trade name Proclaim,, Flubendiamide 24% WG : Trade name Belt. The Principle Entomologist of the Dry Zone Research Station of the Department of Agriculture ( Mrs KNC Gunawardena) has prepared an effective online presentation on FAW control and this has to be shared by all. The African country Ghana has declared a state of emergency in response to this invasion as Maize is a staple crop which should be followed by us in Sri Lanka.
The long term strategies include early detection. Stopping its spread and initiation of a long term research programme to identify tolerant varieties and granting permission to import such varieties as seeds. The country should ear mark on a Biological control strategy by breeding and releasing FAW parasitoids regularly. In USA larval parasitoids such as Apanteles marginiventris, Chelonus insularis and Microplitis manilae have contributed to keep the pest population down along with egg parasitoids Trichrogramma spp and a similar program should be initiated in the affected districts. Finally the best option is to establish a task force with the involvement of entomologists, extension personnel along with the administrators and scientists working in the universities to ensure the country are safe with regards to food security
The author has read for a PhD at University of Florida Gainesville in the USA in 1985 and his PhD thesis exclusively deals on Fall armyworm parasitoids and its ecology
President’s decision on Colombo Port in national interest
by Jehan Perera
President Gotabaya Rajapaksa has announced that the government will be entering into an agreement with the Adani Group, based in India, to offer them 49 percent of the shares in a joint venture company. This joint venture will include Japanese government financing and will manage one of the terminals in the Colombo port. The entry of Adani Group, into the Colombo port, has been opposed by a wide coalition of organisations, ranging from port workers, and left political parties, to nationalists and civil society groups. These groups have little in common with each other but on this particular issue they have made common cause and even held joint protests together. The main thrust of their objections is that control over the East Terminal of the Colombo port will pass into foreign hands and result in an erosion of Sri Lankan sovereignty.
The cause for alarm, among the protesting groups, may be fueled by the observation that one by one, the ports of Sri Lanka are being utilized by foreign powers. In particular, China has entered into Sri Lanka in a big way, obtaining a 99-year lease in the Hambantota port that it constructed. The Hambantota port, in its early period, showed it was economically unviable in the absence of Chinese cooperation. The burden of debt repayment induced the previous government to enter into this agreement which may become unfavorable in terms of national sovereignty. There were protests at the time of the signing of that lease agreement, too, though not as effective as the present protests regarding the change of management in the Colombo port, which is led by the very forces that helped to bring the present government into power.
In addition to the Hambantota port, control over the South Terminal in the Colombo port, and a section of the harbour, has been given to China through one of its companies on a 35-year lease. In both cases, large Chinese investments have helped to upgrade Sri Lanka’s capacity to attract international shipping lines to make use of the port facilities. The Hambantota port, in particular, could benefit enormously from Chinese ships that traverse the Indian Ocean, the Middle East and Africa. Instead of making refuelling stops elsewhere along the way, such as Singapore, they could now come to Hambantota. However, with these investments would also come a Chinese presence that could cause concerns among international actors that have geopolitics in mind. It may be that these concerns are finding expression in the opposition to the Indian entry into the Colombo port.
It will not only be Sri Lankans who are concerned about the Chinese presence in the country’s ports. As Sri Lanka’s nearest neighbour, India, too, would have concerns, which are mirrored by other international powers, such as Japan. It might be remembered that when Japan’s prime minister visited Sri Lanka, in 2014, there was a diplomatic furor that a Chinese submarine entered the Colombo port, unannounced, even to the Sri Lankan government, and docked there. With its excellent relations with China, that go back to the 1950s, when the two countries signed a barter agreement, exchanging rice for rubber, most Sri Lankans would tend to see such Chinese actions in a benign light. In recent years, China has emerged as Sri Lanka’s largest donor and its assistance is much appreciated. However, India’s relations with China are more complex.
The two countries have massive trade links, but they have also gone to war with each other due to territorial disputes. Even at the present time Indian and Chinese troops are in a stand-off on their disputed Himalayan border. In this context, India would be concerned that the Chinese presence in Sri Lankan ports could eventually take the form of an overall strategy to encircle it and use this leverage to India’s disadvantage. Sri Lanka’s location at the bottom of the Asian continent gives it a strategic importance in the Indian Ocean that goes beyond any possible India-China rivalry. The recent visit of US Secretary of State to Sri Lanka included an acerbic exchange of words between the US and Chinese representatives on that occasion and an open call to Sri Lanka to take sides, or not to take sides. As a small actor in itself, Sri Lanka would have no interest in getting involved in international geopolitics and has a longstanding policy of non-alignment and friendship with all.
More than anyone else, President Gotabaya Rajapaksa would be aware of these geopolitical issues. As Defence Secretary, during the years of war with the LTTE, he was a key member of the government team that obtained wide ranging international support for prosecuting the war. Today, the President’s key advisers include those with military backgrounds who have special expertise in geopolitical analysis and who have spent time in leading military academies in different parts of the world, including the US, China and India. This contrasts with the more parochial thinking of political, nationalist and even civil society groups who have come out in opposition to the agreement that the government has entered into with the Indian company to manage the Eastern Terminal of the Colombo port.
President Rajapaksa was elected to the presidency in the context of the security debacle of the Easter Sunday suicide bomb attacks and with the expectation that he would provide clear-cut leadership in protecting the country’s national security without permitting partisan interests from becoming obstacles. In his meeting with the representatives of the trade unions, opposing the handing of management of the Eastern Terminal to foreign hands, the President is reported to have said that geopolitics had also to be taken into account. As many as 23 trade unions, representing the Ports Authority, the National Organisations collective, and a number of civil organizations, have joined the formation of a new national movement named the ‘Movement to protect the East Container Terminal’.
One of those political representatives at the meeting, leader of the Frontline Socialist Party (FSP), Pubudu Jayagoda, is reported to have said, “When trade unions met President Gotabaya Rajapaksa on Wednesday (13), he told them about the broad geopolitical factors in play. This is reminiscent when the unions met former Prime Minister Ranil Wickremesinghe a few years back. The unions told Wickremesinghe what they told Rajapaksa––the ECT could be operated by Sri Lanka in a profitable manner. Wickremesinghe told the union representatives, ‘You are talking about the port, I am talking about geopolitics’.” However, former Prime Minister Wickremesinghe may not have had the necessary political power to ensure that his vision prevailed and failed to ensure the implementation of the agreement.
Entering into the agreement with the Indian company will serve Sri Lanka’s national interests in several ways. By ensuring that India is given a presence in Sri Lanka’s most important port, it will reassure our closest neighbour, as well as Japan, which has been Sri Lanka’s most consistent international donor, that our national security interests and theirs are not in opposition to each other. Second, it takes cognizance of the reality that about two-thirds of the Colombo port’s shipping is due to transshipment with India, and thereby ensures that this profitable business continues. Third, it will give Sri Lanka more leverage to negotiate with India regarding key concerns, which includes Indian support to Sri Lanka at international forums and in providing guarantees for the unity of the country in the face of possible future threats and the need to ensure devolution of power to satisfy ethnic minority aspirations.
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