21 - 004 A Digital Human has his Covid-19 Vaccination

 

There is nothing quite like writing a blog where you can experience first-hand what you are writing about. The nurse was perplexed by this Digital Human being quite excited about getting the COVID-19 mRNA Vaccine BNT162b2 produced by Biontech Manufacturing GmbH. Yes a German manufactured vaccine from a Belgian plant designed by a Turkish husband and wife team at Biontech. At £14.40 per shot. The so called Pfizer – Biontech vaccine. Not the older English technology vaccine called the Oxford Astrazeneca vaccine.

The Digital Human was to receive a piece of new biological technology being pure virus itself in structure as indicated by it being an mRNA vaccine. Yet to be fully proven over time this new approach does not have the years of usage clocked up by the Oxford Astrazeneca delivery mechanism. To this Digital Human to receive a vaccine simply built like the fundamental viruses of life rather than a more complicate concoction makes sense. Keep it simple if possible. Beat the Covid-19 virus with what amounts to a Biontech designed virus. Logically the body will look to attack the Biontech virus designing the  weapons to do so that will be later used to attack a real Covid-19 virus should it enter the body.   

 

Read up this excellent article on viruses. Both the good and the bad viruses.  

https://www.nationalgeographic.com/magazine/2021/02/viruses-can-cause-great-harm-but-we-could-not-live-without-them-feature/

21 - 003 Real Photographs of a Coronavirus

 

At last real photographs of a coronavirus. We have got used to seeing the standard media depictions of the virus where usually an illustrator has produced the symmetrical graphical representation. They usually are made up of very simple geometric shapes and tend to look very symmetrical. Normally a sphere with evenly placed spikes protruding out in a patterned way. Not surprisingly the reality is very different since the cell growth structures in nature are at a cellular level very unstructured and random. Nature does have patterns but at different levels of magnification they vary enormously in their appearance. It is not a surprise to see that coronaviruses have what I term a fluffy cotton wool appearance. It is important to appreciate that down at these nanoscale levels our perception of solids goes into a fuzzy more hairy woolly world. It is quite likely the coronavirus sticks to a human cell in a way more imitating the way a thistle floats in air onto a woollen garment before sticking in place. The nature of movement at a nanoscale level represents itself as being very different to how we see things happening in our human sized world. It is likely that the nanoscale world has its own interpretation of physics. A sort of nanophysics. I am sure the physics laws we have defined in our earthly size of world may be applicable down at a nanoscale. This is why projecting out beyond our world into the universe into the realms of astrophysics also gives us the opportunity to see if our earthly physics rules within our tiny Solar System are still applicable out in the depths of deep space. We may find some different rules out in deep space that may also (or not) apply at the nanoscale level. This brings me back to my favourite subject of consilience but this is not to be explored today.

Look at this Nanographics website where they have taken the output from CryoET images and visually enhanced them using their animation techniques.

www.nanographics.at

CryoET stands for Electron cryotomography that can photograph biological cells in sizes down to below 1-4 nm. The samples being frozen in non-crystalline ice so they can be viewed in a 3D way. These images can be used to build up 3D animations.

http://en.wikipedia.org/wiki/Electron_cryotomography

 

 

 

21 - 002 SARS-Cov2 Variants

 With vaccination now well under way in the United Kingdom (January 2020) it is no surprise that watching out for new mutations of the SARS – Cov 2 virus has been critical. To the credit of the UK Government they have insured the different organisations with expertise in this area have been drawn together and that suitable financing has been agreed to support this important tracking.

The so called “Kent" variant labelled B.1.17 has through its higher transmission rates become a major problem in London and the South East. It includes what was named the N501Y mutation. The virus had continued to propagate at a high rate in these areas whilst the Government rules on lock down remained the same as other areas in the country where propagation was less virulent. Importantly the effective roll out of the testing for the virus has been able to support the provision of excellent localised transmission statistics. This allowing for the genetic surveillance of the virus from area to area within the United Kingdom. This need for surveillance is just as critical internationally with oddly enough South Africa because of its experience with ebola a leading proponent.

So not surprisingly along came the “South African" which also had the N501Y mutation which appears to have developed independently from the Kent variant. But South African variant in addition had another mutation named E484K. Now with the vaccination protecting you by getting in the way of the spike binding with your cells any change in the spike itself has to be a concern. Your immunity depends upon the vaccination generating your anti-bodies and T cells so they interfere or prevent this binding process. Essentially they lower the effectiveness of the spike gaining entry into a human cell.

To get a perspective on the proportions of these viral activities some mathematician has said all the coronaviruses currently infecting the whole world could fit on one teaspoon. I am not sure I can believe this fact nor if it is true can I mentally comprehend it. But what it does do is give you an appreciation of the relative size of the virus.

So we now have a worrying “Brazilian" with both the N501Y and E484K mutations with investigations in progress (15^th January 2021) to determine any other differences. Tracking the RNA structure of these viruses is critical as is seeing how humans react to them in terms of the infection. It is possible that the vaccines may need to be modified and they would need to be applied in a second round of vaccination.

1st February 2021

It is no surprise to hear the "South African" variant has shown up in some more cases in the UK where those with it appear not to have any links to travellers from South Africa. All credit to the UK Government in establishing the COG-19 Genomics (COG-UK) Consortium to deliver rapid whole genome virus sequencing. This is a totally non political blog but you do have to wonder whether some of these "fast scientific and commercial moves" by the UK Government in respect of setting up consortium and the establishing of very early vaccine contracts are down to the new freedoms we are experiencing outside of the EEC where they are showing a decided lack of innovation. 

It now has a World War 2 feel about it with a very British approach to fighting a war where creativity and innovation are backed by the UK Government. It also proves the power of having a National Health Service (NHS) with dedicated health and research professionals as the central controlling (umbrella)  organisation. But most importantly one very focussed upon operating on consortium principles bringing together Universities, Agencies and other Research Institutes. The very British capability of empowering the academic world (the thinkers), the researchers (the creators) alongside the commercial world (the makers )makes for a very powerful entity. What is missing is a more powerful representation of the Information Technology industry. Where are the UK equivalents to Google and Microsoft who of the tech giants are the most "outside of the box" organisations. This is what the UK Government needs to fund next because the virus has now  just been desynthesised down to computer code requiring digital technology investments to complete a major part of the fight back against the virus.          

Read the BBC Report  have 

https://www.bbc.co.uk/news/health-55534727

Look at the this COG  Consortium

www.cogconsortium.uk 

21 - 001 Primeval Soup of Life and the Antibodies Soup

So Boris Johnson, the UK Prime Minister, at 8.00 pm last night (04/01/21) on television announced the 3^rd Lock Down to try and stop the spread of the coronavirus and protect the NHS from collapsing under the pressure of new cases needing hospitalisation. At over 50,000 positive tests for the virus per day with this translating, at a likely 2% death rate, to generating in 4 weeks a death rate of 1000 deaths per day against the available UK beds and importantly the ICU places. Very basic mathematics covering statistics and arithmetic. The only logical criticism should be the decision was late being made since it had hit 89,000 positives on the 29^th December 2020 which should have been the immediate trigger. Lock down is currently the only current way forward until the vaccine can be put in place and in this respect the UK is way ahead of the World. Yet on social media within minutes you see posts rubbishing him and claiming it is all a government hoax to control us more as citizens. Apart from those that oppose everything many of these people just do not understand how a virus works. The fact that you cannot see something that can potentially destroy a good part of the human race is inconceivable to many people.

Now move onto my daily walk in the cold fresh air where my “narrating self” starts talking to me about just about everything. Thanks to Yoval Noah Harari, the author, who introduced me to this “narrating self” expression along with many other insightful things. So the “narrating self” now chooses by itself to follow another pathway of thought. Like there is no cosmic plan. Life has no script. Life has no meaning. During our brief stay on this tiny plant we have many emotions and then we are not heard of any more physically but we may leave digital fragments. But why would anybody look at these digital fragments. It appears to be all a waste of time. Then the mind has these philosophical thoughts terminated by my “experiencing self” where the sight of a woman walking ahead smoking creates a huge plume of smoke which is blown sideways and rises upwards. The “narrating self” returns to analyse this linking it to the exhalation of a virus. It gives a real visual illustration of how extensive human breath can travel beyond the body. Now were she carrying the virus the tiny invisible viruses attached to tiny invisible water droplets expelled from her mouth would be available to transmit to the next person entering into that plume of her breath. Fortunately she was walking well ahead of me. But wearing a mask at all times does make sense.

So back to the “narrating self” and the social media non-believers. It is easy to see that if you step in front of a bus you can get run down and killed. The Government has created laws to define how the roads are used. In the same way the Government has created laws to protect us from a virus. No different. The problem is people cannot see the virus coming whereas they can see a bus. So let us look consider this virus scientifically.

It has got a name from the bioinformatics community of SARS-CoV-2 and it is at the bottom level of life based upon RNA. It exists in the primeval soup of life but it has come up through a chain of DNA life acting as a carrier possibly via a bat to gain entry into us humans. Now within this primeval soup it would have constantly changed to maintain its survival within this soup. Once moving up through a chain of transmission it would have changed forming new variants to continue this survival. Not a believer in any cosmic plan they are just random chemical processes that can generate different outcomes. But we now have the scientific capabilities to track these changes and to see the digital code underlying them.

Boris Johnson’s announcement followed scientific evidence that a new “UK variant” is more transmittable whilst there appears to be a “South African variant” that is even more transmittable. Measuring and comparing transmission rates is not easy since it is dependent on the effectiveness of mass testing. The number, accuracy and record keeping of these tests.

The mutations to create the variant are in the virus’s spike protein. This spike protein alone can be considered to be like a string of about 3000 beads folded into a complex three dimensional structure to form the spike. Now this spike is interesting. Is its entry into the human cell dependent on it being a “beak” or “key” or “pad”? The beak would suggest some mechanical becking, the key something that fits into a membrane lock or a pad suggesting a chemical agent on it that dissolves some local human cell membrane. Reading the latest research the idea of a key seems the most popular. As a key the spike must fit with a receptor, the lock is called Ace2, which sits on the surface of the cell membrane. To me it seems very important to establish exactly the physical process of entry. For example one suggestion is the South African one is “stickier” one assumes meaning it holds on better for longer to gain entry.

The virus is continually making copies of itself and in this replication process changes can randomly occur some of these benefitting the virus whilst some do not. The process of evolution then supports those that are made more effective whilst those less effective die off. It is a continual cycle guaranteeing the strongest or most effective succeed.

Now these changes can be digitally defined with the digital code changed in the virus identified. Consider the virus to be like a saved word document where the text (code) can be changed and then saved as a different file name. So these spike mutations have resulted in many different file names. Within the UK and South African they have been identified as N501Y being one of the changes within the spike. This maybe just one of the 3000 beads making up the spike being differently set. The N501Y change seems to be popping up across the world in unconnected settings suggesting it seems to be a very common naturally forming mutation. Sort of if you reproduce enough times it is likely to be an error that often occurs but then it prospers so further reproductions automatically include it from the start.

Now some of these spike mutations can be worrying particularly when they might reduce the effectiveness of the vaccine. There is one school of thought that believes that once you start vaccinating the human bodies anti-bodies get produced more readily and with the virus more exposed to them it might mutate to counter the attack into something that more lethal. The spread of this more lethal virus would then evade the effects of vaccination.

One such mutation has been named K417N which has prevented a type of monoclonal antibody taken from a recovered patient from attacking the virus. The virus effectively resisting this antibody. Another called E484K has also shown signs of making some antibodies less effective against the spike. Now this is where the term primeval soup can be used again. Vaccination causes the body to create a soup of different antibodies to fight the virus and this takes place within a healthy body where the virus has not got hold. The human bodies antibody soldiers supported by a healthy body can focus upon the destruction of the invader virus. When the virus has got hold of someone making them unwell then the antibody creation mechanisms result in the loss of their effectiveness.

For those suffering from the virus it makes your “narrating self” try to understand what your “experiencing self” is going through and it is not nice. Your body is taken over with all your control over it lost to what will be your ultimate fate. To those on social media it is not the Government that control your destiny it is your hourly or daily decisions you make that are the only things that may have an impact on your life expectancy. It is your personal virus avoidance plan that matters. But this is within a cosmic backdrop that is beyond everybody’s control. It was no wonder religions were once very popular since science offers you no peace of mind. But one sure fact is that your death is inevitable one day from something.

20 - 030 Digital Human Reflection

So let us reflect on the Digital Human blog produced through 2020. When I made my first blog on this subject on 19^th January 2020 little did I know at the same time the coronavirus epidemic was starting to take hold in Wuhan, China. It would be my blog (20-011) dated the 29^th April 2020 titled “Digital Invaders” where I first discussed coronavirus as a result of me going down with similar symptoms from 23^rd February 2020. I clearly remember saying to my wife, Jenny, what I am experiencing is far from the normal flu. I felt very different. My thought processes were unable to access fully what was going on other than I felt something had taken over my body. Below is my Personal Diary entries for this period:-

Sunday 23/02/20	Start of cold like symptoms at a family christening in Coventry.
Thursday 27/02/20	Getting worse. Doctor’s appointment. Prescribed Amoxicillin.
Wednesday 4/03/20	Now very unwell. No taste or appetite. Low energy levels.
Sunday 8/03/20	Did not get washed or dressed. Too exhausted.
Monday 9/03/20	Very unwell. Doctor’s appointment. Chest X-ray requested.
Tuesday 10/03/20	Took to my bed. Not well enough to sit up. Had to lie down.
Friday 13/03/20	Chest X-ray clear. Water sample and Bloods OK.
Saturday 14/03/20	Family to Moat House for a meal for Emma’s 16th Birthday
Sunday 15/03/20	Felt very unwell as I woke up.
Monday 16/03/20	Not normal yet but feeling a bit better. Had a piece of toast.
Tuesday 17/03/20	Got up at 6.30 am and made Jenny a cup of tea. First Time.
Tuesday 17/03/20	Lock Down imposed for UK by Boris Johnson. Prime Minister.
Saturday 21/03/20	Still suffering a congested chest.

 

Inevitably my blog now steered to the subject of this coronavirus. As the media focussed upon this subject I was able to access a great deal of very current and relevant information. But having experienced what I have come to assume was coronavirus the whole subject took on a new relevance. This was further accentuated when my business partner, George Szubinski, was hospitalised with coronavirus and died on the Tuesday 14^th April 2020. George had his first test for coronavirus on Friday 20/03/20 and it was negative. He was hospitalised on the Friday 27/03/20 with a positive test and discharged on the Sunday 5/04/20 with a negative test to only be re-hospitalised on Friday 10/04/20 to die on the Tuesday 14/04/20. His wife Janis was in the same hospital with coronavirus at the time of his death. George had no major underlying health concerns but his body reacted very differently to coronavirus. Was it the anti-body attack escalating out of control after defeating the coronavirus that finally caused his death? The medical profession has now come to appreciate the importance of the use of anti-inflammatory drugs in the management of coronavirus. Management of the anti-bodies is now a critical part of the recovery process.

Now upon reflection this Digital Human blog has got hijacked by coronavirus. Now this does not matter. I had never set out to produce a true “blog” with the need to post to a regular timeline. It was always intended to be a structured way of note taking in support of the book I am writing called the Digital Human. The blog had no followers or readership and this was never its intention anyway. But unfortunately it was now not meeting the needs of my note taking. It had started to become a bibliography or more specifically a web link repository linking to the digitised resources I was researching. It was also moving away from any logical structure that I would need in my final book. So a rethink was required for 2021. It also occurred to me that if I could automate the blog into the production of an eBook and Paperback this could be a paid for or free resource which could trigger the marketing of the final Digital Human book. There was also a realisation that the final book could never be a completed piece of work. It was under dynamic and continual change. So it had to adopt a more Wikipedia constantly updated approach so the facts communicated were the latest. But at the same time Wikipedia lacks the “story” element and just the facts so it is not a very good learning or educational tool. The Digital Human has to be a learning and educational book. It’s a book not a website since I want it to have some permanence about it. It can be an eBook but it must have a parallel Paperback copy to give it real physical permanence.

So this started me thinking about what was the Digital Human book in terms of its scope. It was not an encyclopaedia which is just facts. It needed to have a story element but I am not an enthusiast of authors that paint emotional pictures before launching into the subject matter. But I do like authors that set out in a story like way the historical context. Even looking to generate reader emotion within this historical context is acceptable. I must admit I like the author Kevin Kelly’s approach to technology and biology where he often uses stories relating to his life in California which gives you the reader some memorable links to the facts he is communicating. This is especially the case when you live in a cold and wet England.

Whilst I am not keen on the use of what I term invented academic vocabulary. These invented fashionable “words” often created to support the directions taken by the academic community now forced into being as business like as any of the other communities. They need complex and new course names to attract the new students to show they are, as educational institutions, aligned with the real world outside of academia. I preferred it when it was pure academia avoiding trying to be a business.

Research from academia through to commercial organisations and the new alliances generate new words to act as the “coat hangers” for the researchers allowing for a short hand approach to ever more complex and detailed subjects. The world of the research community. Then to the vocabulary of the media and publishing industries. The commentators on everything else. New words to adorn new “Smart Thinking” book covers to entrap the reader to buy. New words for newspaper and magazine and now website and social media headlines and banners. Anything in a bigger font. Anything to attract the reader’s eye.

Then finally my own profession of the digital (computer) industry where the commercial segregation of new paid for marketplace is often defined by new technological terminology. The paid for consultancy of the non-technological organisations into these mysterious subjects that are never mysterious just being digital bits structured differently by the enlightened ones (ie experts or consultants) who have only named them differently. The digital industries now generate their own vocabulary by the hour along with the biological industries. A subset of the digital industry is the information industry and within this it is no surprise to see bioinformatics becoming the commonly used word to describe the application of computational technology to handle the rapidly growing repository of information related to molecular biology. The word fits perfectly with what the Digital Human book is looking to achieve. But I want to be a bit more pure in terms of what is Digital Human is looking to achieve. It’s going be a possibly going to be a folksonomy or taxonomy. But the word that really fits for me is it is an ontology.

The Digital Human book is going to be an ontology. For me this combines information science and philosophy to represent entities, ideas and events with their interdependent properties and relations according to a system of categories. Sounds complex and it is complex. But most importantly those working on artificial intelligence (AI) acknowledge the importance of building knowledge engineering upon which to build the AI. Importantly deciding it is an ontology gives me a framework on which to build the Digital Human book.

Now there are so called “Frame Languages” to support creating an ontology. They are similar to hierarchies in object orientated languages fortunately an area I am familiar with in terms of business computing systems. Now in the world of knowledge representation (KR) and artificial intelligence (AI) the use of a modern Web Ontology Language (OWL) is the recommended technique. Now I am not going to use these languages. But in writing my Digital Human book I am going to bring the structure and text in line with these frameworks. This is important since it lends some peer based credibility to the book. The book may then lend itself to giving direction and content to the use of OWL. But most importantly I want the Digital Human book to meet the needs of a general readership and not one specifically biological nor informational.

The difficult area for me is I have not defined in my mind the overall structure of this Digital Human book yet. As I write these words (04/01/21) I am still formulating a structure for the book. Current thoughts are a zoom down through the human passing systems, organs, cells to atoms. A top to bottom as a hierarchical structure but ending up with the DNA code. Then a similar top down view on the natural decay, faults and invaders looking to shorten the life of the Digital Human. Finally a developmental “life cycle” view going from conception through cell multiplication through to a normal living stasis then through to aging and decline to death. Medication, life style and diet were to be plugged into this “life cycle” as possible pathway changers or improvers. The mechanical parts, whose you can handle however small, need to be separately defined but where these parts are the more complex like the brain, nervous and hormone systems they need another deeper type of entity type. Consciousness within the brain is going to be a subject in its own right. Then something that I have called the “wireless” entity needs defining with this remaining a very uncharted and to some people, in fact most people, this is considered a non-existent element in terms of analysing life. Currently not sure how all these will be structured into the Digital Human book. The best policy is to make a start and evolve the approach as I develop the content through 2021.