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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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Sinharaja world heritage

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Conservation Outlook Assessment: Significant Concern

By Professor Emeritus Nimal Gunatilleke

Continued from Yesterday

 

Water diverted from Ampanagala reservoir to Muruthawela will be used to meet the irrigation deficit of Muruthawela and Kirama Oya systems and the balance will be transferred to Chandrika Wewa, through existing LB canal of Muruthawela scheme up to 13.8 km and a new canal of 17.0 km. After that, the water requirement of Hambantota harbour is to be transferred to Ridiyagama tank through the Walawe river and Liyangasthota anicuit. However, due to the extreme length of the diversion through the three-river basins of Nilwala, Kirama Ara and Urubokka Oya, it will lead to a massive conveyance losses of the diverted water while on the way to the Walawe basin. Furthermore, enormous costs associated with its construction, a failure to fully realise the intended outcomes due to a shortage of water budget will simply be a burden that Sri Lanka cannot afford with her current economic condition, according to Eng. Prema Hettiarachchi. It may be worth recording that the water ingress into the grouted tunnel of the Uma Oya near Ella has still not been fully repaired, even though the Uma Oya project is nearing completion. An expensive lesson to be learnt on the nature of the weathered geological structure, lineaments and implementing its unexpected and costly mitigatory measures which will eventually to be paid back by this and future generations of tax payers of this country.

According to the Irrigation Department web site postings, Mahaweli Consultancy Bureau has initiated the Environment Impact Assessment (EIA), but due to the unavailability of concurrence of the Forest Department, revised TOR has not been issued by the CEA. Therefore, due to the unavailability of updated TOR, the EIA study has been delayed.

Environmentally, the most contentious issue highlighted in the news media is the proposed construction of a RCC dam at Madugeta to build a reservoir for which around 79 ha of forested (and some agricultural) lands in Sinharaja and a portion of prisine riverine forest in Dellawa would be inundated. On the Sinharaja side of the proposed Madugeta reservoir (right abutment) at present there are home gardens and small-scale tea plantations in addition to good riverine forests. In contrast however, proportionately a larger area of luxuriant forest of Dellawa, which is a part of the new ‘Sinharaja Rain Forest Complex’ would go under the chain saw for this reservoir construction (left abutment). The Geo-engineering report of May 2019 on GNDP has revised the siting of the dam to a more favourable location with supposedly reduced impacts but they forewarn that the three core-drilling along the proposed dam axis that had to be temporarily abandoned due to protests made by the villagers, need to be completed to confirm the geological suitability for the dam site.

 

Are there any Environment-Friendly Alternative Options?

As an alternative site for a dam on Gin Ganga, Eng. Nandasoma Atukorale (Specialist Engineer [Hydropower]) has proposed a location at the confluence of Mahadola with Gin Ganga at the village of Mederipitiya, way back in 2006. According to him, the riverbed at this site is 261 masl and have a catchment area of 132 km2. He proposes the construction of a 35 m high concrete gravity type dam that would form a reservoir with a storage capacity of 65 million cu.m and a potential discharge of 320 million cu.m of water annually which could divert 293 million cu. m of water to the SE Dry Zone. Most importantly, this region passes through a relatively narrow section of the river which is ideally suited for a dam according to him. However, geological suitability and socio-economic impacts of local communities need to be investigated, beforehand.

Quite interestingly, Eng. Athukorale claims that ‘although it is not economically very attractive, another 200 million cu.m of water could be diverted to the Nilwala basin by constructing a dam across Gin Ganga at the downstream of the confluence with Dellawa Dola at the village of Madugeta, with an 8000 m long tunnel which could be considered at a later stage provided further water shortages are experienced in the area’.

 

Now that the proposed Madugeta reservoir is receiving heavy criticisms from the environmental front, wonder whether Mederipitiya option proposed by Eng. Athukorale could be revisited for the diversion of Gin-Nilwala river water to the SE Dry Zone.

In a research paper titled ‘Comparison of Alternative Proposals for Domestic and Industrial Water Supply for Hambantota Industrial Development Zone’ Eng. Prema Hettiarachchi makes a comparison among three irrigation projects Kukule Ganga, Gin-Nilwala and Wey Ganga to convey water from the SW wet zone to SE dry zone.

She proposes yet another option that is probably still on the drawing boards to be considered which is the Wey Ganga diversion in Ratnapura District. According to her, this could meet the industrial and drinking water requirement (154 MCM + drinking water) of Hambantota metropolitan area at a significantly lower cost and with less damage to the environment. Further, there is a possibility of augmenting this scheme by diverting a part of Kalu Ganga catchment at a later stage.

Eng. Hettiarachchi further states that ‘by comparing the workload, it could be estimated to be nearly one third that of the Gin-Nilwala diversion. The Wey Ganga diversion can be carried out at a significantly lower cost by local agencies. That can also address the water scarcity of Hambantota metropolitan area including the requirements of international harbour and proposed industrial development zone with the relatively less environmental damage which is a major issue with respect to large scale projects. Construction period will also be less since the workload is less and can be carried out by the local agencies’.

What I have strived to show with this detailed irrigation engineering information available on public domain in the form of research publications, is that the Madugeta reservoir option is not the only one available for taking water from the wet zone rivers to the SE Dry Zone which is indeed a legitimate requirement for agricultural and industrial development of that region.

Pre-feasibility studies have been conducted on these options since 1968 and a considerable wealth of technical information is already available with the Irrigation Department. Apparently, according to knowledgeable irrigation engineers, there are more environmentally friendly, and cost-effective options with greater assurance of water conveyance to the SE Dry Zone available for consideration. It is often the case that during pre-feasibility studies of these large engineering projects, environmental concerns are given the least priority. Steady supply of water during extreme drought events which are becoming more frequent depends very much on the nature of the vegetation cover of the watershed area. These environmental aspects need to be critically evaluated before such costly projects are designed. As an example, although, the major engineering work of the Uma Oya project has been almost completed, its cost-effectiveness is yet to be seen with a denuded watershed, a potential of heavy soil erosion on top of the unexpected heavy expenditure on tunnel boring and other engineering works.

Biologically speaking, the Dellawa Forest Reserve is an integral part of Sinharaja Rain Forest Complex representing the pristine climax forest vegetation of SE wet lowlands and provide a vital connectivity link to adjoining Diyadawa forest of equal significance via the remains of Dombagoda forest. Therefore, clearing a riverine strip of this forest for the construction of Madugeta Reservoir would lead to an irreparable and irreplaceable damage to its characteristic riverine/flood plain forest vegetation.

On the other hand, pledging a reforestation initiative of a much larger area with Hevea rubber as a compensatory measure proposed by the political administration is totally unacceptable. Preserving intact forests in protected areas has no substitutes or replacements. Furthermore, the Natural Heritage Wilderness Area act and the binding articles of the UNESCO Convention on Protection of the World Cultural and Natural Heritage to which Sri Lanka is a signatory, clearly state that causing direct or indirect damage to a natural heritage is legally not permissible.

In summary, the Sinharaja World Heritage Site is already in a state whose biological values are threatened and/or are showing signs of deterioration and significant additional conservation measures have been recommended to restore these values over the medium and long term. Adding more threats like the construction of reservoirs inside protected areas at this stage would inevitably downgrade the values further to a ‘critical conservation outlook’ which is not what the citizenry of Sri Lanka and the world at large would acknowledge as ‘sustainable development’.

The author of this article is a member of the National Sustainable Development Council of Sri Lanka and he thanks Dr Jagath Gunathilaka of Peradeniya University for providing the geotechnical information described herein. The author can be contacted at .)

 

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US seeking way out of Afghan killing field

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As the Biden administration makes its initial moves to extricate the US’ remaining security forces personnel from Afghanistan, it would do well to ponder on former US President John F. Kennedy’s insightful comment on foreign policy: ‘Domestic policy can only defeat us; foreign policy can kill us.’ This is a rare nugget on the nature of foreign policy.

Considering the high costs, human and economic, a country could incur as a result of blundering on its foreign policy front, Kennedy could be said to have spoken for all countries. However, there is no denying that the comment is particularly applicable to expansionist powers or ‘hegemonic’ states.

Sensible opinion is likely to be of the view that the US decision on quitting Afghanistan should have come very much earlier; may be a couple of years after its bloody misadventure in the conflict and war-ridden country. Considering the terribly high human costs in particular the US’ 20 long years in Afghanistan have incurred, the US could be said to have committed one of its worst foreign policy blunders, overshadowing in severity the blood-letting incurred by the super power in Vietnam. However, in both theatres, the consequences for the US have been of unbearable magnitude.

The US death toll speaks for itself. At the time of writing more than 2,300 US security forces personnel have been killed and over 20,000 injured in Afghanistan. Reports indicate that over 450 Britons have died in the same quagmire along with hundreds of similar personnel from numerous other nationalities. Apparently, it took an exceptionally long period of time for the US to realize that Afghanistan for it was a lost cause.

The lesson that the US and other expansionist powers ought to come to grips with is that it would not be an ‘easy ride’ for them in the complex conflict and war zones of the South. The ground realities in these theatres are of mind-boggling complexity and Afghanistan drives this point home with notable harshness. Power projection in South-west Asia and persistence with its ‘war on terror’ were among the apparent prime objectives of the US in Afghanistan as well as in Iraq but what the US did not evidently take into consideration before these military involvements were the internal political realities of these countries that are not at all amenable to simplistic analyses and policy prescriptions.

The Soviets ought to have come to grips with some features of the treacherous political terrain presented by Afghanistan in the late eighties but their principal preoccupations were related more to the compulsions of the Cold War. Simply put, the Soviets were bent on preserving the ‘satellite’ status of Afghanistan and their war effort was aimed at this in the main. Preparing Afghanistan for democracy was not even least among the Soviet Union’s concerns, of course.

However, the same does not apply to the US. The latter helped the Mujaheddin in the task of getting rid of the Soviet presence in Afghanistan but its aim was also to have a US-friendly regime in Kabul that would be a veritable bridgehead of US power and influence in the region on a continuous basis. In other words, the US expected the regime which replaced the Soviets to be pro-Western and essentially democracy-friendly. The US did not in any way bargain to have in Afghanistan Islamic fundamentalist regimes whose political philosophies were the anti-thesis of democracy as perceived in the US and practised by it.

However, the Islamic fundamentalist Taliban regime which eventually came to power in the mid-nineties in Afghanistan, once the Soviets withdrew, defied all Western expectations. As is known, the Taliban was not only repressive and undemocratic but was staunchly opposed to everything Western. There were no hopes of the Taliban working towards Western interests. Besides, the US did not expect to see in Afghanistan a country dangerously divided on ethnic, tribal and religious lines. The problems of Afghanistan have been compounded over the years by the coming together of the Taliban and the Al-Qaeda and these groups have world wide Islamic fundamentalist links.

It has been the aim of the US to have in Kabul religiously moderate, pro-democratic regimes but as developments have proved over the past few decades these administrations have not been in a position to hold out against the Taliban. In fact, it is the Taliban that is veritably at the helm of power in Afghanistan currently and years of futile attempts at trying to contain the Taliban have brought home to the US and its allies that they have no choice but to talk to the Taliban in order to secure some respite to effect ‘an honourable exit’ from the bloodied land. This is where matters stand at present.

However, as pointed out by commentators, it is the Afghan civilian population that has suffered most in the decades-long blood-letting in the country. Conservative estimates put the number of Afghan security forces personnel killed in Afghanistan at around 60,000 to date and the number of civilians killed at double that figure.

Accordingly, the Afghan people would be left to face an uncertain and highly risk-riddled future when the last of the US security forces personnel and their allies leave Afghanistan in September this year. The country would be left to its own devices and considering that the Taliban will likely be the dominant formation in the country and not its legitimate government, the lot of Afghan civilians is bound to be heart-rending.

There is plenty to ponder on for the US and other democratic countries in the agonies of Afghanistan. One lesson that offers itself is that not all countries of the South are ‘ready for democracy’. This applies to very many countries of the South that already claim to be democracies in the Western sense. Southern ‘democratic’ polities defy easy analysis and categorization in consideration of the multitude of identity markers they present along with the legitimacy that they have achieved in the eyes of their states and populations. What we have are dangerously volatile states riddled with contradictions. Relating to them will prove to be highly problematic for the rest of the world.

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The Soul

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The Soul (also known as Ji hun) is based on the sci-fi novel ‘Soul Transfer’, written by Jiang Bo in 2012. The novel was widely popular and inspired director Cheng Wei-Hao to adapt the tale into a movie. The story is about a married couple who are determined to uncover the truth behind strange activities in their community. According to the official synopsis for the film from Netflix, while investigating the death of a businessman, a prosecutor and his wife uncover occult secrets as they face their own life-and-death dilemma. The film stars Chang Chen, Janine Chang and Christopher Lee among others.

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