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Viruses and Life on Earth

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Abrupt changes in the number of living animals in past millennia? Major dips indicate mass extinctions following cataclysmic events (last one: picture above uc.sc). Minor dips represent declines in dominant species likely to be caused by viral pandemics

By prof. Kirthi Tennakone

National Institute of Fundamental Studies

Viruses exist everywhere in association with living things, decisively influencing their evolution as well as behaviour. A virus secures a message encoded in its genome by a cover of proteins and lipids – carrying a warning, as if written and kept in a sealed envelope to be opened.

When a species attempts to be too smart by exploiting common resources and procreate endlessly; the virus intervenes to control the expansion.

Pandemics and epidemics caused by viruses had adversely affected humans, colonies of animals and cultivations. Nonetheless, the mission of viruses to alert species to not monopolise and expand; appears to be a crucial factor that diversified and preserved life on earth. What viruses do today to teach us is painful, but they were our progenitors and saviors.

If not for viruses and pandemics they created in the past; we ourselves and lively animals and plants around us would not have existed. Viruses may also have acted as the precursor agent which created life.

The origin of life on earth, its evolution into species has been shaped by viruses. Until humans evolved, viruses did not permit one species to dominate and rule the earth. They might dictate terms to us in future and sway our destiny.

 

Origin of viruses and origin of life

How viruses came to being remains a puzzle intimately connected with the mystery of the origin of life. Although life occurs everywhere on earth in different forms and perhaps in planets circling distant stars – what life means, evades rigorous and consistent definition. Generally, entities capable of storing information and replicate by digestion of substances in the environment are considered as living. Another characteristic of life is the aptness to undergo Darwinian evolution – the inherent capacity to mutate into variants so that ones fitting the environment survive and reproduce. For this reason, United States National Aeronautics and Space Agency (NASA) defined life as self-sustaining chemical system capable of Darwinian evolution. In terms of above interpretations; viruses fall outside the domain of living systems, because they can replicate only by entering a living cell and hijacking its machinery to reproduce. Unlike bacteria, viruses cannot grow in dead animal or plant tissue. Possibly they stand in between living and non-living, based exclusively on ribonucleic acid (RNA) when they first originated. Quite a number of present day pathogenic viruses are also RNA based.

RNA is a chain like motif decorated with four different types of molecular beads referred to as nucleotides bases, denoted by symbols A, C, G and U. The sequential arrangement of the beads encode information; just like a message written in a four letter alphabet language.

According to one school of thought, viruses came first and evolved into advanced forms of life. Later they learned to invade living organisms as parasites. This idea supports RNA hypothesis of the origin of life, where most primitive replicating biomolecules were considered to be forms of RNA; naturally synthesised out of nucleotides floating in prebiotic oceans.

If viruses came first; why did they resort to parasitism later? Possibly as life in prebiotic oceans advanced evolving into cellular organisms; chemical substances essential for primitive viruses to breed were exhausted, forcing those viral variants with a taste for cellular life to proliferate.

Viruses are the smallest self-replicating entities; size ranging from 200 – 400 nanometers (1 nanometer = one millionth of a millimeter), but their reproduction happens inside a living cell. Recently several types of giant viruses, larger than 1000 nanometers and comparable to size of an average bacterium has been discovered. Amazingly these giant viruses self-replicate, just like unicellular microbes without a host cell – suggesting virus-like entities finally evolved into advanced forms of life. The very thing from which we may have been created is now threatening us!

How viruses infect cells?

Viruses attack animals, plants, bacteria and all the other cellular organisms. They are host specific; a virus sickening an animal, rarely infect humans directly. The host specificity generally depends on ability of the pathogen to bind or attach to the host cell membrane. To impregnate genetic information, the virus must affix itself to the tissues of the host. Viruses have acquired intricate strategies to invade the cells by this mechanism. The outer shell of a virus known as the capsid serves to protect its genome. The structure of the capsid and proteins there have evolved to anchor the virus into specific sites in host tissue known as receptors. In the case of the corona virus, a protein in the spikes bind to a receptor on the host cell membrane named ACE2 – kind of protein found in a wide range of human cell membranes – notably those in mouth, nose, throat and lungs.

After binding to the receptor, virus injects the genetic substance to the interior of the cell. Viral RNA or DNA (some viruses are DNA based) intermingle with DNA of the cell. Thereafter, the virus commandeer the cell to obey instructions written in its genome and make copies of itself, using energy and resources of the cell. The sickened cell burst open releasing virus particles, which infect other cells. The above process, known as the lytic pathway of viral reproduction, kills the host cell. Sometimes virus inside the cell, replicate when the cell divides, via so-called lysogenic mode of reproduction. Lysogenic reproduction helps virus to evade host immunity and prolong the infection. Coronavirus is lytic, whereas the HIV virus switches from one mode to the other.

Virus variations: the ability viruses to undergo genetic changes

The invasive potential of RNA viruses rests largely on their inherent flair to undergo genetic changes frequently to exploit Darwinism. When a RNA virus replicate errors would occur in the sequence of the nucleotide bases A, C.G and U. For example the sequence AACU may be wrongly copied as AACG. Such accidental changes or mutations alter the character of the virus progeny. Often the mutations turn out be ineffective or deleterious to survival of the virus; but occasionally, the variant (one produced by mutation) may acquire qualities more favorable for its proliferation, such as resistance to host immunity or faster transmission. The probability of a mutation in a RNA virus per replication exceed that of a host organism million fold. Furthermore, viruses replicates at rates orders of magnitude faster than the host and their numbers are astronomically larger. Thus in the case of RNA viruses the likelihood of emergence of variants spreading faster would be significantly high. That is why in a period less than two years we have seen several potentially dangerous variants of the coronavirus. More people getting infected and longer the pandemic lasts; the chances of virus mutating to variants is higher.

Viruses also have disposition to undergo major genetic changes described as antigenic shifts. When different viruses infect the same cell, a segment of RNA from one virus could get inserted into the genome of the other as a recombination. Some viruses have more than one strands of RNA, in this situation, strands could be exchanged by a process known as re-assortment. Spanish flu virus is believed to have originated by re-assortments involving viruses from avian, swine and human sources.

When we allow opportunities for the virus to breed; we are at the risk of being confronted by new mutant variants or antigenically shifted strains that spread even faster. The strategy a virus adopts to achieve this objective may inadvertently turn out be a more virulent attack that escalates the death toll. Virus gains no benefit by being virulent.

Host congregation and overpopulation

Despite the advantage of fast mutability (Darwinian superiority), viruses predisposes a frailty. They being delicate and minute; cannot survive outside host for very long; without getting denatured by heat, sunlight and other environmental conditions. As such, viruses find hard to move from one host to another, unless the hosts position close proximity to each other.

If a kind of animals or plants dominate segregating into densely populated colonies, at the expense of common resources to be shared by other species; viruses invariably gain access to the system, sometime or other, creating an epidemic or pandemic! The result would be limitation of the population, but not up to the point of extinction; because when the susceptible host population thins out as a result of immunity and deaths, the virus stops spreading. In the vacant niches opened – up, other varieties of plants and animal flourish. Even the original affected species, may regain strength and reappear. Thus far, because of ingenuity, humans have succeeded in evading the eventuality of this phenomenon, but for how long?

From prehistoric to modern times, pandemics have abetted the diversity of life and paved way for social reforms. Similarly, past extinction events had eventually made the world of flora and fauna more diverse and sustainable.

History tells when destructive calamities end or made to retract; new opportunities surface – communities of organisms have progressed that way.

Extinctions and aftermath

Fossil records reveal life on earth suffered several mass extinctions wiping out a large percentage of plants and animals in a short time. Planetological evidence points to the conclusion; volcanic eruptions, climate change and an asteroid impact as the causes of the major destructions. In between mass extinctions there had also been more frequent minor ones indicative of disappearance or marked decline of the population of some species. Arguments have presented to explain these endangerments to as viral pandemics.

Mass extinctions events initially interrupted life drastically curtailing the diversity. Amazingly habitats recovered – diversity regained or increased beyond the original index.

The Permian- Triassic extinction originating from catastrophic volcanic eruptions in Siberia 252 million years ago, killed over 90 and 70 percent of marine and land animals. In about six million years; biodiversity regained, new species adopting more advanced life styles appeared.

The extinction that changed the world for ever was caused by impact of an asteroid 66 million years ago. Gigantic dinosaurs who dominated the world for millennia vanished leading the way for mammals to takeover. Perhaps viruses helped our ancestor mammalians to establish by killing medium size reptiles survived the asteroid catastrophe, but immunocompromised by food shortage – opening the way for humans to evolve. Brain became more important than the body size and one species dominated the biosphere. Human innovation succeeded in resisting natural forces limiting the undue expansion of the species. They controlled illnesses, cultivated crops on large scale, using science based techniques. However, maintaining a population continuing to increase, present new challenges; because we are getting vulnerable to the same natural predicaments which limited the growth of animal populations.

In between major extinctions arising from environmental calamities, there were more frequent disappearances of many species. When animals and plants overpopulate, viruses intervene to bring forth pandemics, limiting the population. Are we approaching a similar scenario?

Emerging zoonotic diseases and future pandemics

Everyone knows COVID-19 is caused by an agent termed a virus. Viruses are all over latently hiding in the bodies of animals and humans. Infrequently, dependent on environmental conditions, a virus from an animal could move to a human, get adapted to the new host and cause an epidemic or a pandemic. Almost all previous viral epidemics and pandemics including measles, rubella, smallpox, Spanish flu initially surfaced in this manner are said to zoonotic in origin.

Zoonotic diseases or zoonoses reached epidemic proportions when humans segregated into settlements, as viruses spread when hosts live close together. Settlers domesticated animals; close contact transferred pathogens from animals to humans. Measles is believed be the dog distemper virus adapted to humans and Spanish flu a zoonosis associated with pigs and birds.

Following industrialisation and multiplication of urban localities of increasing population density, more zoonotic diseases turned into epidemics. Polio has been an ancient disease but epidemics did not occur until early 20th century. Dengue spread all over tropics; beginning late 1960s, when urbanisation congregated people into cities.

Dengue, chikungunya, zika and other existing or emerging insect vector mediated viral infections poses a severe threat for of the following reason. Insects are a very successful species. They have stubbornly survived all mass extinctions, since they evolved 500 million years ago. No other widespread species has been exposed to viruses for so long and as such they have acquired strong innate immunity to viruses. Therefore, they can harbor viruses asymptomatically, without getting manifestly sick and transfer the virus to vulnerable humans and animals.

Recently, within a short span of time, a number of zoonotic diseases have emerged; Ebola, Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), Avian flu (H5N1), Zika, Nipah and lately COVID- 19 . When greedy humans encroach habitats occupied by animals or spoil the environment by their activities; wild life has no alternative than to move closer to humans. The viruses causing the diseases; SARS, MERS, Nipah and COVID -19 are believed to have disseminated from bats, when their habitats got disturbed. Rearing farm animals in torturous congested conditions, create situations conducive for them to catch infections of wild species and transfer them to humans after genetic modifications. Loss of biodiversity create conditions favorable for zoonotic disease to emerge and turn into epidemics for pandemics.

So many species of animals and have gone extinct because of anthropogenic activities and millions are threatened. On this scale, viruses have not exterminated a single species – they only limit unwarranted expansion of species. We are accustomed to think that the non-living senseless virus is the culprit; when the real cause has been our behavior.

In 1901 the French Chemist Le Chatelier enunciated a principle, which goes after his name. Le Chatelier’s principle states “If a system is stressed, the system reacts in such a way to relieve the stress “. If the system is taken as the collection of flora and fauna of the biosphere and stress as human activities endangering the biosphere; it follows from the principle that natural forces in the biosphere will react to human activities. The present pandemic and emerging zoonotic diseases are example of such reactions.

World needs to be prepared to counter pandemics. Swift action once they emerge would not solve the problem as the virus may propagate and mutate much faster than our response. Vaccines are proven to be effective. Understanding required to design vaccines and installing manufacturing plants and rolling inoculations to the global population takes years. The real offender that bring forth pandemics is our behavior. Environmental destruction, occupation of the habitats of wild species and unwarranted congregation at all levels of association, prompts pandemics to emerge and propagate. The other factor is ignorance and irrationality of thought, continuing to prevail – many advocate myth and pseudoscience. The pandemic is a signal that humanity needs to adjust and change collectively for betterment.

 

 



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Features

English in Mathematics

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By R.N.A. de Silva

 

“Which subject did you have most difficulties with, having switched the medium of instruction from Sinhala to English?” I posed this question to a Sri Lankan student who was following a pre-University course in an educational institution in Hong Kong, having completed studies up to the GCE Ordinary Level programme in the Sinhala medium in a leading girls’ school in Colombo. “It is definitely mathematics,” she replied. Having served as a teacher for a long period of time at this educational institution with students from over 80 countries, I realised the above-mentioned view was shared by other students, too, who had to change the medium of instruction to English. This does not seem to make sense as one would have expected mathematics to be the easiest subject to follow as it has its own symbolic language. Why then has this situation arisen?

I would like to separate these difficulties into two categories:

1. Hastiness due to mindset

2. Vocabulary issues

Sometimes hastiness can automatically occur due to the mindset that mathematics should be easy to follow even if you change the medium of instruction as you are dealing with symbols. This attitude can cause enormous problems as students may skip instructions or avoid reading the question fully and concentrate only on the symbolic part of the problem

As an example, consider the following question.

The graphs of lines 3y = 5x + 1 and 2y = 7 – 3x intersect at point P. Find the coordinates of P.

Seeing the word ‘graphs’ and the two equations, a student maybe tempted to draw the graphs of the two lines and thereby find the point of intersection, which is a time-consuming affair. If it was read properly, the student could have noticed that the solution can be obtained by solving the two equations algebraically, which is much more efficient.

To a fast reader, obtaining the correct answer to the following question can be a problem as it may end up with just finding the value of x.

If 2x+3 = 5x-3, find the value of 2x+3.

The students need to be trained to read the question fully and understand what is required to be done, before attempting it.

The time spent to grasp the aim of the question is not wasted time.

Many children consider mathematics as an alien language consisting of symbols and expressions. Most of the difficulties that students encounter is related to vocabulary. The mathematical interpretation of the meaning of a word may differ from the meaning given to it in the English language. The word ‘find’ in mathematics means to obtain an answer showing the working while in the English language, it refers to discover or search. The following sketch shows the funny side of this difference.

Two of the words that has caused much confusion are ‘or’ and ‘and’.

In general usage, A or B is considered as either A or B but not both, as shown in picture.

However, in mathematics ‘A or B’ means ‘it can belong to A or B including intersection’. This is shown in picture.

The above, in normal usage is interpreted as ‘A and B’. However, in mathematics A and B refers to only what is common to A and B as shown in picture.

Here are the mathematical meanings of some of the other words which can have a different meaning with the English language definitions.

Determine

– Obtain the only possible answer

Plot

– Mark the position of points on a diagram

Write down

– Obtain the answer (Working need not be shown)

Constant

– A number that does not change

Similar

– Having the same shape but not the same size

Deduce

– To show a result using known information

Operation

– A procedure such as addition, subtraction, multiplication, etc.

Element

– A member of a set

Volume

– The extent of space occupied by a solid

The following illustrate some of the difficulties that the difference of meanings brings:

How odd these odd numbers are? The even numbers are even stranger.

Don’t be mean and help me to find the mean of these numbers.

Is right angle the right answer? Let me write it on the board.

The polysemous nature of some of the mathematical terms make it confusing for the students in the understanding of mathematical concepts. Mathematical terms have precise definitions to describe numerical relationships. At times these definitions resemble the everyday usage meaning but there are instances where the definitions notably differ. Consider ‘in general’ as an example. In mathematics there can be no exceptions to a result if it is considered to hold in general. However, in everyday usage, if a claim is said to be true in general, it would mean that it is true most of the time, but exceptions are possible.

To add to the problem, there are some terms such as ‘degree’ that can have many different meanings within mathematics while having a different meaning in everyday use. In mathematics, degree can refer to the measurement of an angle, the complexity of an algebraic equation and a unit of temperature.

Although mathematics deals essentially with symbols, it is taught through the medium of language which is the major means of communication. Students build understanding as they process ideas through language. It is important for students to give emphasis to the familiarisation with the mathematical vocabulary and at the same time understand the difference of meanings of terms mathematically and everyday usage. Teachers have an important role to play here in highlighting such terms and using them in different contexts for comfortable acclimatization. As Marcus Quintilianus quoted, “One should not aim at being possible to understand, but at being impossible to misunderstand.”

(The author is a senior mathematics examiner of the International Baccalaureate Organization and a member of the faculty of the Overseas School of Colombo.)

 

 

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Features

Success with debut single

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Fred-James Koch: Lots of airplay for ‘I’m Runnin’

 

Fred-James Koch seems to be more in the news, these days, than his illustrious father, Alston Koch.

The turning point in Fred-James career is, undoubtedly, the Hollywood film ‘Night Walk.’

His role in the film is two-fold – actor and singer.

It’s, in fact, his singing of the theme song, ‘I’m Runnin,’ that has generated quite a lot of excitement, among music lovers.

The song is now being heard, world-wide, over radio (in Sri Lanka, on Sun FM), while the video, too, has been seen by many, on social media.

An Australian magazine, ‘Music Injection,’ had this to say about Fred- James:

“Fred- James Koch has written an incredible theme song for the movie ‘Night Walk,’ called ‘I’m Runnin.’ Just released, this song is engaging and gives us a sense of urgency, as the song builds. Fred-James vocals have a unique tinge to them and with the video having scenes from ‘Night Walk,’ it encourages me to watch the movie. ‘I’m Runnin’ features AZ Sheriff.” – Jen.

Following the debut spin for ‘I’m Runnin,’ on The Music Director programme, on 88.3 Southern FM Melbourne, the track was also played on the All New Saturday Ausmosis programme.

And, guess what! It’s now No. 3 on the Australian Top 20 Download chart. and No. 2 on the Australian Top 20 Stream chart.

 

 

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Inklings of change in national reconciliation policy

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By Jehan Perera

 

The government comfortably overcame a vote of no-confidence in one of its key ministers over the rise in the price of fuel.  Those who expected to have greater numbers supporting the no-confidence motion miscalculated that the apparent differences and rivalries within the government would be uppermost.  Any government, or institution for that matter, would have its internal differences.  The current government is better secured against these differences that might otherwise split it into different competing parts on account of the familial bonds that bind the leadership together.  The President, Prime Minister, newly appointed Finance Minister, as well as the former Speaker who is now Irrigation and Internal Security Minister, are closely knit brothers who have gone through trials and tribulations together. 

An iconic photograph of recent times would be the joy on (then) President Mahinda Rajapaksa’s face when he embraced his brother (then) Defence Secretary Gotabaya Rajapaksa shortly after the latter survived a suicide bomb attack at the height of the war.  The brothers, however, have different strengths and constituencies.  They have different groups who follow and advise them, and each of these groups would prefer if their leader was the first among equals.  President Gotabaya Rajapaksa’s comment that he has another eight years in which to achieve his goals has been widely discussed.  It would send a signal to others in the polity that it would be premature to gather around another member of the family at this time in anticipation that the baton would be passed on at the conclusion of the President’s current term in 2024.

On his part, the President has been promoting the institution he once served and to which most of his confidantes belonged or continue to belong.  The institution of the military is one where the closest of human bonds can be forged, because on the battlefield each depends on the other for their lives.  In his early period in office, the President has been promoting the military, both serving and retired, wherever he can, as ambassadors to foreign nations, as Covid health guideline monitors and as a supra grade of administrators in government departments.  It is often the case that those appointed to these positions are not the best suited to the tasks they have been set to do.  But the President evidently trusts them and they are his support base.  Unlike any other president in the past, President Gotabaya Rajapaksa is not a member of a political party.  Civil society organisations have periodically called for a non-party presidency who is non-partisan in decision making. 

 

CHALLENGE EXCESSSES

However, there is a need to challenge the excesses.  The president’s pardoning of a soldier who was held by several courts, including the Supreme Court, to have deliberately killed children and (adults, eight in all), outside of the battlefield may be due to his conviction that loyalty to the military counts most.  However, the President is expected to uphold the system of checks and balances, and if he favours one institution at the expense of the others, it leads to a weakening of the entire structure of governance.  Another looming challenge is that posed to the autonomy of institutions of higher education and specifically the universities.  The government decision to vest the Kotelawala Defence University with powers to accredit other institutions of higher education is a threat to the freedom of thought and expression.  The military hierarchy who will head the KDU can be expected to have values that are important to the military, but not to democracy which is based on human rights.

The KDU law needs to be opposed as indeed the Federation of University Teachers Associations (FUTA) has urged along with opposition political parties.  At the same time there are other issues on which civil society can consider giving constructive support to governmental initiatives.  For instance, they do not engage with NGOs who provide a variety of services complementing the work of the government. The most important of these is the national reconciliation process.  There are indications that the government is shifting its stance on the issues of post-war reconciliation.  President Gotabaya Rajapaksa’s election victory on a highly nationalist platform won him a big majority of votes of the Sinhalese ethnic majority.  The government felt empowered to publicly declare its intention to withdraw from the post-war reconciliation process initiated by its predecessor government with support from the international community.  This was followed by withdrawal from UNHRC resolution 30/1 of 2015 co-sponsored by the previous government. 

However, the four subsequent internationally driven resolutions against Sri Lanka, emanating from Geneva (UNHRC), Ottawa (Ontario Parliament), Washington DC (US Congress) and Brussels (EU Parliament) seem to have led to a serious rethink within the government about its policy towards post-war reconciliation.  All four make human rights and the ethnic conflict their centerpiece.  Though not yet publicly commented upon, the signs of change are two-fold.  The first is the increased visibility of the US Embassy in meeting with the leaders of the Tamil and Muslim parties.  The media has reported that US Embassy officials discussed issues of post-war reconciliation efforts, devolution of power, rule of law and the Prevention of Terrorism Act with SLMC leader Rauff Hakeem. Recently, a US Embassy delegation, led by Ambassador Alaina B. Teplitz, held similar discussions with TNA leader R. Sampanthan where the focus was on the proposed new Constitution.

 

CHANGING WINDS

The second sign of a change is the statement from the Presidential Secretariat announcing a recommendation, emanating from the President Commission of Inquiry for Appraisal of the Findings of Previous Commissions and Committees on Human Rights and the Way Forward headed by Justice AHMD Nawaz.  This is with regard to the EU call for the abolishing of the Prevention of Terrorism Act long seen by those promoting national security as part of the country’s first line of defence.  The Commission said that it cannot agree with calls for repealing the PTA but Sri Lanka’s anti-terrorism law should be reformed in line with similar laws in other countries, including the UK.  This would be aimed at affirming Sri Lankan sovereignty and national security interests, which are important to the government’s voter base, while complying with the requirements of the EU parliament which has called for the repeal of the PTA on the grounds that it violated human rights. 

The Presidential Secretariat statement also contains a significant section in which it mentioned that “It is the policy of the Government to work with the United Nations and its agencies to ensure accountability and human resource development in order to achieve lasting peace and reconciliation. The Government is committed to providing solutions for the issues to be resolved within the democratic and legal process and to ensure justice and reconciliation by implementing necessary institutional reforms.”  This is the first official indication that the Government is reconsidering its earlier position that it would blaze is own path with an indigenously generated reconciliation model which would not require international assistance. In this context it would be useful if the government focused closer attention to the achievement of the UN Sustainable Goals.

Veteran Tamil political leader V Anandasangaree, who has championed Tamil rights for a long time, and whose son is a Canadian parliamentarian, has referred to these recent developments and said that the President who holds the defence portfolio, Prime Minister and Finance Minister being members of Rajapaksa family could ensure genuine post-war reconciliation.  He also urged President Gotabaya Rajapaksa’s government not to leave the problem for a future administration to resolve, but address it now.  If the President is to successfully address the problem that has eluded a solution since independence, and been the biggest disaster to Sri Lanka’s development, he will need to broad base his support at multiple levels.  He will not only need the support of the ruling party, led by his brothers, as well as civil society, but also that of the ethnic minority parties and the opposition political parties.  This will require patience, dialogue and self-sacrifice, and the need to break from past and chart a reconciliatory course of action.

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