virology

•

10 weeks since having Covid-19 I had two blood test where my CRP (C Reactive Protein) was < 5. CRP is produced by the liver and is a sign of inflammation in the body due to infection or other conditions such as heart disease or autoimmunity. This is a sign of a recovery from Covid-19. This is something you should have routinely checked when you visit your GP -- it is a simple blood test.

I was fortunate not to have encountered  the complications mentioned in my previous posting about Covid-19. I attribute this to life-style factors. I live in a peaceful retirement village within 11 hectares of beautifully maintained gardens and surroundings. One can step outside into the sunshine and be washed over with the feeling of being one with the Universe.  I’ll forebear from  breaking out into song like Julie Andrews: “the hills are alive with the sound of music”. But you get the general idea of this whenever you experienced the natural sounds and beauty of a walk in nature.

The other factor is having an energy view of the world, complimented by non-materialism.. This is a cosmological view which I’ll not elaborate on here, but will leave it for future blog postings. Suffice it to say that it includes the energy of the Universe, the Chi, something briefly mention in previous postings. This was not a sudden molecular virologist’s “conversion on the way to Damascus” but a gradual move towards Shiva’s molecular dance as described by Fritjof Capra. This  borders on Panpsychism, a theory that suggests that consciousness is a fundamental property of  the Universe, another topic to explore further.

In an effort to avoid falling into the several rabbit-holes mention above, I’ll go straight to the work of Donna Edna and her energy healing. Donna’s approach is: here are the exercises, do them and you can heal yourself. No mumbo-jumbo, no change in beliefs necessary, no secret sauce, no secret handshakes involved. She does offer several courses and further instruction but they are not essential since the body knows how to heal itself. A simple daily 5-minute routine is provided below by Donna Eden and David Feinstein.

Some of the topics introduced here will be explored in future Blog posts: cosmology, panpsychism, consciousness, and fundamentals of the Universe. Some of these topics are also expounded upon at: https://cosmickiwi.com.

•

One of the consequence of having had Covid-19 is the predisposition of becoming depressed. 

The World Health Organisation noted this year that anxiety and depression increased by 25 percent across the globe in just the first year of the Covid-19 pandemic.  In a 2021 study, more than half of American adults reported symptoms of major depressive disorder after a coronavirus infection. The risk of developing these symptoms — as well as other mental health disorders — remains high up to a year after you’ve recovered. One major explanation for the increase is the unprecedented stress caused by the social isolation resulting from the pandemic. Linked to this were constraints on people’s ability to work, seek support from loved ones and engage in their communities.

It’s possible that Covid-19 may even compromise the diversity of bacteria and microbes in the gut. Since microbes in the gut have been shown to produce neurotransmitters like serotonin and dopamine, which regulate mood, this change could be at the root of some neuropsychiatric issues. Gut bacteria manufacture about 95 percent of the body's supply of serotonin, which affects the mood and the feeling of Zing. 

Serotonin and other neurotransmitters travel from the gut to the brain via the vagus nerve. The body's longest nerve that emerges directly from the brain. Magnesium works as an important co-factor required for conversion of tryptophan (from proteins we get from food) to serotonin and melatonin. (Note to self: Must increase my intake of magnesium at night.)

•

 

(NOTE: ZING = a quality that makes something exciting, interesting,: it is enthusiasm or energy).  

I am 84 years of age and in the fourth week of recovery from a severe Covid-19 illness. I am gradually getting over that zinged out feeling - that grey and shady feeling that life is too much of an effort.

 t wasn’t just the virus bit, but a host of co-morbidities that contributed to my urgent rush to the Emergency Ward. The precipitating evident was my losing my balance and falling backward and hitting the hallway wall with the back of my head — resulting in the punching of a hole in the wall and a stunned feeling of surprise. I was found to be Covid-19 positive, severely dehydrated, with pneumonia  and urinary incontinence. (An aside: I had never been hospitalised for an illness before and was surprised that at my age and stage, I was asked to sign a “do not resusitate” form.) I was put on a saline drip (6 litres later) and antibiotics intravenously. I was in the Covid-19 isolation ward for 3 days. 

I lost 7 kg (15 lbs) during this time and the long-lasting, chronic  lung infection is only now beginning to clear. My voice is returning to its usual self and  I may not need a second laryngoscopy of the vocal cords to remove some nodules. (An aside: I was developing a squeaky voice presumably due to modules on the voice chords and had an operation to remove some of them.) A feeling of zing is beginning to creep into my psyche or perhaps it is the Chi of Taoism. 

An aside: In Taoism Chi is a primal substance that animates the universe I— a mysterious force introduced to us by ancient Chinese myths.


Hospital food -- dinner!

•

Why viruses?

“If all viruses suddenly disappeared, the world would be a wonderful place for about a day and a half, and then we’d all die – that’s the bottom line,” says Tony Goldberg, an epidemiologist at the University of Wisconsin-Madison. “All the essential things they do in the world far outweigh the bad things.”

•

 

There is nothing like a graphic to explain a concept in molecular virology, such as how mRNA vaccines work.  The need to have mental images was explained in a previous post -- Wittgenstein and Cosmology

The BioNTech-Pfizer and Moderna vaccines use the mRNA that codes for the SARS-CoV-2 spike protein. This mRNA can be made in copious amounts in the laboratory but RNA is notoriously unstable and be easily degraded by RNAse enzymes and room themperature. The packaging into lipid nanoparticles adds to its stability and keeping it a freezing temperatures prevents the RNA being broken down by the ubiquitous presence of RNA degrading enzymes.

Injection of the vaccine into the arm delivers the mRNA into cells where the lipid nanoparticle fuses to the cellular lipid membrane layer and delivers the mRNA into the cytoplasm of the cell. The ribosomes bind to the mRNA and produce multiple copies of the CoV-2 spike protein. This spike protein migrates to the cell membrane and stimulates the immune response.

The main cost of the vaccine is the need to store the mRNA at low temperatures, the Moderna vaccine  can be maintained at most home or medical freezer temperatures while the BioNTech-Pfizer vaccine requires -70 degree ultra freezers.  No doubt there will be improvements in methods to stabilise these mRNA vaccines and reduce the costs.

This mRNA technique can also be used for future pandemics and the lipid nanoparticle provides a ‘plug and play’ for any virus. It potentially can be used for other immunotherapies such as for cancer, cystic fibrosis and other systemic and congenital diseases.

As Gwynne Dyer wrote in a recent column, “we can now be sure that the light at the end of this particular tunnel is not an oncoming train”.

For more graphics see NATURE Vol 580 pp 576-7, 2020
OR https://www.phgfoundation.org/briefing/rna-vaccines

• 1 Comment

•

In order to understand the significant of this question some background is required. During this lockdown period we have had an opportunity to reflect on our ‘essential priorities’ and the kind of world we would like to live in. It is not just a manner of going back to ’normal’ since that normal was not all that great for a large portion of humanity. We are also heading for a climate change disaster, there are huge income inequalities in most countries and the ‘for profit’ capitalism is not providing for the health and social requirements for a ‘just and fair society’.

The Back Story

Over the last 15 years or so, David Jones, a retired professor of microbiology and I have been meeting for lunches on a fortnightly basis during which we discuss the state of the world and contemplate the cosmos. David in his retirement has become interested in cosmology and the evolution of the universe and I would expound the idea of the fifth force of the universe, the force of intelligence. By and large we agree on the standard model of the four forces in the universe (the strong nuclear, the weak nuclear, the electromagnetic and the gravitational) and the overall outline of the Big Bang model of the universe.

David takes issues with many of the details of the Big Bang and the things that the model does not explain and proposes alternate scenarios to explain Black Holes, dark matter and the ‘flatness’ of the universe. I invoke the force of intelligence to explain how the universe works. I will let David explain his theory of cosmology in his own words in a future blog post, but I shall attempt to explain the force of intelligence in the following brief paragraphs.

The force of intelligence

Having a Taoist predisposition to seeing the universe as self-organising and naturally flowing along intelligence lines, the universal law of intelligence proposed by Wissner-Gross  seemed imminently sensible. He proposed the equation:

F = T ∇ Sτ to explain this new fundamental force. In the equation, F is a force that acts so to maximise future freedom of action. It acts with some strength, T with the diversity of possible accessible futures, S, up to some future time horizon, τ (Tau). In short, intelligence maximises future freedom of action and keeps options open. It not only correlates with the production of long-term entropy, but actually emerges directly from it. The force carrier is the intelligon (my notation) much like the photon is for electromagnetism.


The results of the force intelligence are to maximise the future freedom of action and keeps options open. We cultivate open minds not because we are liberal or conservative, young or old, but because we understand intuitively that it is a matter of survival—physically, emotionally and intellectually—to maximise access to future possibilities. This occurs at all levels of biology, the physical and the cosmological world.

We as humans have a high level of consciousness and are sometimes awe-struck as we look up at the universe and are moved to feel at One-With-The-Universe. We can at first hand have the experience of the force of intelligence. Intelligons are the force carriers of this and carry information between things and how to behave. As photons give us light, intelligons are the information. (Here is where we encounter difficulties in using commonly used words to describe new and novel ideas. This is why the use of the language of mathematics is easier — but then we are not mathematicians. But indulge me for awhile and suspend your preconceived ideas and the ordinary meanings of the words.) At present we have no ways of measuring the force of intelligence and it is only recently that gravity waves (gravitons) have been detected but there are manifestations of the force of intelligence all around us from cityscapes to molecular biology.

From our understanding of the weak and strong nuclear forces and the electromagnetic force we have created not only destructive nuclear weapons but all manner of wondrous electronic devices that turn night into day and project images and information around the world. With internet connectivity we can link all of humanity into an interacting — dare I say an intelligent entity. As an aside, it is interesting that Issac Newton, a Trinity College student at Cambridge was sent home to continue his studies during the 17th century Black Plague pandemic. During this ’social distancing’ he used his time wisely and worked on the theory of gravity,



Intelligent systems

The earth has often been described as a Goldilock planet. It has the right proximity to a star allowing liquid water; is a rocky planet; has the ability to support an atmosphere neither too thick or too thin; has a magnetosphere strong enough to protect the atmosphere from Solar Wind stripping; temperatures that change not too little and not too much from night to day; diversity of life creating a food chain; tidal action from a large moon; a stable central star; an atmosphere with an ozone layer; both land and water on a surface with more water than land.

James Lovelock and Lynn Margulis in the 1970s developed the Gaia Hypothesis which conceived of the earth as a self-regulating system. The idea of a world having a planetary Logos, is ancient and is found in both Eastern and Western cultures. Gaia is usually conceived as a "formative force," an active, intelligent, purposeful presence at work in the material world to guide and guard the course of planetary evolution — the force of intelligence.



The story so far

The first human ancestors appeared between five million and seven million years ago, probably when some apelike creatures in Africa began to walk habitually on two legs. They were flaking crude stone tools by 2.5 million years ago. Then about two million years ago some of them spread from Africa into Asia and Europe. Then about 200,000 years ago, Homo sapiens emerged. In a relatively short period of time humans have taken dominion over the planet and we are now living in the Anthropocene period. This geological age can be viewed as the period during which human activity is the dominant influence on climate and the environment. This is not good news since human activity is causing the deterioration of the environment through depletion and pollution of air, water and soil; the destruction of ecosystems and habitats; the extinction of wildlife species; ocean acidification; global warming; ozone depletion — the list goes on.

Where does Covid-19 fit in?

The novel SARS-CoV-2 coronavirus emerged in the city of Wuhan, China at the end of 2019 and has since caused a large scale Covid-19 pandemic that has spread to 70 countries. The first known coronavirus to cause severe illness in 2003 was know as SARS (Severe Acute Respiratory Syndrome) emerged from China after humans contracted the virus after direct exposure to civets. A second outbreak occurred in Saudi Arabia and became known as MERS (Middle East Respiratory Syndrome) after direct exposure to camels. SARS-CoV-2 is very similar to a bat coronavirus but there is no evidence of direct bat to human transmission. There are suggestions that intermediate hosts such as pangolins or civets or ferrets were involved. This leaves the possibility that future outbreaks of illness causing strains of the virus could be circulating in animal populations and could once again jump into humans.

The conditions of the ‘wet’ markets in China where several species of animals are kept alive in cages under very stressful conditions provided ideal conditions for animal cross-infections. These are man-made profit-orientated situations that should be banned as bad practice and made illegal. The coronavirus in bats probably only causes a mild illness and may be useful for bats in combating predators which may intrude on their ecology.

YES

Is Covid-19 a cosmological event? The answer is YES. Habit destruction and the extinction of wildlife species has been a key factor in the emergence of Covid-19 as well as HIV in West Africa and Ebola in the Democratic Republic of Congo. These actions can be seen as going against Gaia, the active, purposeful presence of the force of intelligence at work. When a society doesn’t invest in a sound healthcare system with safety nets for the underprivileged, protective equipment for emergencies, etc it will reap the results of those decisions.

YES, we will eventually be able to control Covid-19 using drugs and vaccines. But it will take years to repair the economic and social damage. YES, we will still be susceptible to the next pandemic virus emerging from wild animals.

YES, Covid-19 has caused us to pause in a global lockdown and forced to think about what is essential in life post-Covid-19. There is not a simple way to reset things to what they were before because things were not that good before Covid-19. During this pandemic governments were finding funds for healthcare, innovations in education and communications, wage subsidies towards a universal living wage and social support. Why not for a better future?

YES, even global companies such as Amazon, Google and Apple will need to reconsider their bottom-lines; it can not only be for profits and that they must have a social responsibility as well.

AND after Covid-19 we still have the problems of climate change.

•

This video is from the science of HIV.

This blog post is about the life cycle of HIV (Human Immunodeficiency Virus) that illustrates the need to add another universal force to the current four (strong and weak nuclear, electromagnetic and gravitational) namely: Intelligence. That intelligence operates at all levels, including the cosmological. It does not require consciousness or life. It is the anti-entropy force that leads to complexity and the evolution of everything within the universe.

One usually doesn’t think of viruses as having intelligence. Intelligence is more usually associated with animals that have complex brains and nervous systems. In a previous blog post I used the example of a simple bacterial RNA virus, MS2 as an example of the intelligent behaviour of a string of 3569 RNA nucleotides wrapped in a protein shell. I explained how the virus used the ‘noise’ (error-rate) of ribosome translation to orchestrate the timing, the order and quantity of its gene expression. (The flip-side of what is normally considered to be entropy or chaos.)

The life-cycle of HIV is much more complex and with the aid of an animation (see above) we can visualise the interactions of its many components with that of the cell in the life cycle — the manifestation of intelligence at the molecular level..

The back story to HIV

Back in ’60’s Howard Temin, as a research postgraduate student,  worked on an RNA tumour virus, Rous Sarcoma Virus. This virus causes tumours in chickens. Using tissue culture cells, he observed that mutations in the virus caused structural changes in the infected cell. He proposed in his PhD thesis that this RNA virus replicated via a DNA ‘provirus’. This upset the widely held belief at the time of the "Central Dogma" of molecular biology of Watson and Crick -- that the sequence of information flows from DNA to RNA to protein and never from RNA or protein to DNA.

In 1969, Temin showed that RNA tumor viruses carried the enzymatic ability to reverse the flow of information from RNA back to DNA using reverse transcriptase. Reverse transcriptase was also independently and simultaneously discovered in association with the murine leukemia virus by David Baltimore at the Massachusetts Institute of Technology. In 1975, Baltimore and Temin shared the Nobel Prize of Physiology or Medicine. This group of viruses containing the enzyme reverse transcriptase were classified as retroviruses among which HIV is an important member.

The discovery of reverse transcriptase is one of the most important of the modern era of medicine,  Reverse transcriptase is the central enzyme in several widespread viral diseases such as AIDS and Hepatitis B. Reverse transcriptase is also an important component of several important techniques in molecular biology, such as the reverse transcription polymerase chain reaction, and diagnostic medicine.

This animation, as well as giving the general public some idea of how HIV replicates, illustrates the awe-inspiring molecular intelligence of this virus and is an example of the force of intelligence at work in the universe.

• 2 Comments

•

CRISPR is causing a major upheaval in biomedical research.  It is cheap, quick and easy to use, and it has swept through labs around the world as a result.

What is CRISPR? - it is an abbreviation for ‘clustered regularly interspaced short palindromic repeats’. It was  initially found in bacteria as a resistance mechanism to foreign genetic material such as plasmids and phages.

CRISPRs are associated with cas genes that code for proteins related to CRISPRs —  Cas9 for instance  By delivering the Cas9 protein and appropriate guide RNAs into a cell, the organism's genome can be cut at any desired location. Researchers only need to order the RNA fragment; the other components can be bought off the shelf. Total cost: is as little as $30. This effectively democratises the technology so that anyone can use it.

Last year, bioengineer Daniel Anderson of the Massachusetts Institute of Technology in Cambridge and his colleagues used CRISPR in mice to correct a mutation associated with a human metabolic disease called tyrosinaemia. It was the first use of CRISPR to fix a disease-causing mutation in an adult animal — and an important step towards using the technology for gene therapy in humans.

What are the risks?

Many researchers are deeply worried that altering an entire population, or eliminating it altogether, could have drastic and unknown consequences for an ecosystem. They are also mindful that a guide RNA could mutate over time such that it targets a different part of the genome. This mutation could then race through the population, with unpredictable effects - the risk of the accidental release of an experimental gene-drive.

What is a gene-drive?

First let us look at how mutations are normally spread within  populations.

STD-1

With gene-drive the genetic change would spread rapidly throughout the population since at each mating the genetic change would occur in both parents.

GDI-1

For further information, the source article is: Nature 522, 20–24 (04 June 2015)