The following was sent to the Otago Daily Times
Can Australia and New Zealand make the Trans-Tasman Bubble work? Will they be able to keep these passengers separate at their international airports from those travelling from red-zone countries? The answer is: probably yes. Both countries have experience in herding sheep.
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
This post is a follow on from the previous one which used the word intelligence to denote the 5th force of the universe. For those that have just joined, here is the back story so far.
For the past 15 years, David Jones (a colleague who is also retired) and I have been meeting for lunch on a fortnightly basis. During these lunches we solve the world problems of the day and then settle on to cosmology. David has taken on the task of revising the ‘standard model’ of the Big Bang and I have been trying to expound my theory of there being a 5th force of the universe -- the force of intelligence. This force is present at the fundamental level of quantum mechanics and is as pervasive as the forces of gravity and electromagnetism.
We come up against the usual problem of trying to describe new concepts using ordinary everyday language -- trying to give new meanings to old words. This was a problem that Ludwig Wittgenstein, an early 20th century philosopher, grabbled with and failed to succeed. He considered his philosophical works a waste of time, gave away his vast family wealth and became a reclusive and taught school in some remote part of Norway. He had a similar view of Bertrand Russell’s work, Principia Mathematica. Bertrand was Ludwig’s PhD supervisor at Cambridge.
Wittgenstein's view of philosophy was that it floundered at the meaning of words and the use of language. According to him, we communicate by using mental pictures of what we mean. We need those mental pictures in order to communicate. In trying to describe something new like the 5th force of nature, using words like consciousness or panpsychism or intelligence immediately brings a lot of baggage with it and different kinds of images in the mind of the listener. In order to free oneself from old images new words need to be coined and new mental pictures to go with them.
A candidate word for the 5th force of the universe is LOGOS. In ancient Greek philosophy and early Christian theology, Logos represented divine reason implicit in the cosmos, ordering it and giving it form and meaning. Its usage here in cosmology is free from the philosophical and religious contexts but does give it the flavour of a force of nature that has intelligence and consciousness properties,
Drawing a picture of this 5th force of nature is challenging but it can be placed alongside the other forces in the table below:
We now come to the problem that Wittgenstein so clearly stated when it comes to describing something entirely new, “whereof we can not speak, we must pass on in silence.” And it is reminiscent of the first few lines of the Tao Te Ching “The TAO that can be spoken of is not the TAO itself. A description of the TAO would require a duplication of the TAO.”
LOGOS, the 5th force, embodies the total intelligence of the cosmos. It is the emergence of properties of matter from subatomic particles, quantum mechanics, to atoms, to molecules, composition of rocks, molecular biology of living things, stability of chaotic systems, the red spot of Jupiter, the lifting of consciousness to the rapture of poets, the feeling of awe and oneness with the universe. Its wonder and manifestations are one and the same.
Like gravity it operates at the cosmological level but it also operates at the quantum level. Does it explain the fundamental problem of the ‘observer effect’ in quantum physics -- the double slit experiment? When there is no observer, the atoms fired one at a time form the inference pattern of waves
but when an observer is present, they form two bands as they pass through the slits -- waves/particles..
The best mathematical description of LOGOS so far is that made by Wissner-Gross and his equation for intelligence: F = T ∇ Sτ. In his 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, Tau. In the words of Wissner-Gross: “Intelligence should be viewed as a physical process that tries to maximise future freedom of action and avoids constraints in its own future.”
Like the diagram of the space-time continuum of Einstein, the force field of LOGOS encompasses the cosmos by connecting everything in a quantum entanglement.
We are accustomed to living in the electro-magnetic force field with sunlight, radio waves of all lengths, infrared (heat) waves, X-rays, microwave towers, bluetooth. We use electromagnetism in our electric motors, smartphones, computers and electric toothbrushes without giving them a second thought. The force field of LOGOS pervades our culture, the arts, our sciences and every aspect of our intellectual life. It is present from the quantum world to the vastness of the cosmos.
It has been described that certain individuals like Steve Jobs and Elon Musk are able to bend reality -- they are hooked into this force. This is probably how the mystics contemplated the universe from time immemorial.
Maybe with the force of LOGOS we will not need dark energy and dark matter to prop up our current understanding of how the universe works.
That is LOGOS, the 5th force of the universe described in a nutshell. Having given the 5th force a word and some concepts, this becomes the beginning of the story and further discussions will evidently follow. (I can also hear the mutterings of dissent from the scholars of the Classics and maybe software programmers but hopefully they can see the problem of assigning the right word(s) to this force.)
Personally I’ll continue to use ‘the force of intelligence’ and sometimes consciousness when talking about the 5th force as outlined in the Table above. I also intend to go through the Tao Te Ching and pick out some insightful descriptions for the 5th force of the universe.
Now like Wittgenstein, it is time to “pass on in silence”
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’.
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.
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,
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 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.
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.
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.
You are probably one of the 2.32 billion active Facebook users and see this as a convenient way of keeping in touch with friends and family. Also you probably use Google and YouTube to keep up with the news and events of the day. You know that they are the BIG DATA BEHEMOTHS of the world and that they are collecting data about you. But you view them as benign entities engaged in clickbait advertising activities — after all they have to earn money in some way to provide you with all these free services. Little do you suspect them in propagating false information or fake news or that they are the handmaidens of vested interests that are disrupting what remains of our liberal democracies.
We need to take heed of the DATA BEHEMOTHS and climate change.
According to David Attenborough we have 10 more years before the dangers of climate change began to disrupt societies. A good example of these warnings is illustrated in the TED Talk by Carole Cadwalladr.
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.
You don’t need a degree in molecular biology to follow what is happening in genetics. This animation helps to illustrate the way CRISPR-Cas9 works and how it can be used beyond gene editing. Cas9 and its different fusion partners can increase or block gene expression, facilitate specific base changes or illuminate the genome.
A 'community town hall type meeting' was held on September 17th, 2017 in the St David Lecture, University of Otago to discuss daisy drive technology. The meeting was chaired by Professor Gemmell who leads the Trojan female technique for NZ pest control.
Kevin presented a talk which illustrated the technology of daisy chain drive in lay terms and invited the public to become involved and to share their suggestions, concerns, and criticisms. How should this technology be tested for safety and stability? Where should field tests take place and how should they be monitored?
This open and community-responsive development approach is planned to be the polar opposite of the traditional closed-door strategy used for engineered crops. He left the audience with the following points to consider as pros and cons.
Daisy drive: reasons in favour
- humane: no poisons required
- local and species-specific
- open, community-guided research
- already committed to removing invasive rodents
- success would ultimately eliminate engineered genes
- development doesn’t mean agreeing to deployment
Daisy drive: reasons against
- mostly theoretical
- unclear how to test spread and stability in the lab
- hard to predict outcomes of ecological change
- genetic control may have international complications
- some object to genome engineering
- may conflict with Maori values or be unsuitable for other reasons
Kevin emphasized the high risks that New Zealand might face from the international community who may impose non-tariff trade barriers or from individuals who might seek to illegally introduce genetically modified animals into their own country. He cited the example of the illegal introduction of rabbit calicivirus from Australia to New Zealand in 1997.
For further information, see the Responsive Science website for New Zealand predator-free.
The Department of Conservation has set a target for New Zealand to become pest free by 2050. This includes mice, rats, stoats, rabbits and possums. This is very unlikely to be achieved using the conventional methods of poisons, diseases, traps, shooting or other such methods.
Previous posts have described the use of genetic drives to control pest populations (Trojan Female Technique) and CRISPR global gene drives.
However, as Kevin Esvelt explains: "the problem with current CRISPR-based gene drive systems is that they can spread indefinitely. That means releasing a handful of organisms could eventually affect every population of the target species throughout the world. It's unclear how these systems can be safely tested.
Standard drive systems spread indefinitely because a single piece of DNA encodes the desired alteration, the CRISPR system, and instructions to cut the original DNA sequence. In cells that produce sperm or eggs, CRISPR cuts the original version, causing the drive construct to be copied in its place. All of the organism's offspring will inherit a copy, editing will happen again in the offspring, and the process repeats until the drive system has spread through most or all of the population.
In daisy-chain drive systems, the CRISPR components are split up and scattered throughout the genome so that none of them can be copied on its own. Though physically separated, they're functionally arranged in a linear daisy-chain: element C causes element B to drive, and element B causes element A to drive.
Element C doesn't drive, so its abundance is limited by the number of daisy drive organisms released. Natural selection will gradually eliminate C from the population. That means B will initially increase in abundance, then decline and vanish. In turn, A will increase even more rapidly, but eventually will run out of B and disappear -- as explained in the video above."
For more on Daisyfield Gene Drive Systems
A Community Meeting to discuss Daisy Drive Technology is being held in Dunedin, New Zealand on September 17th, 2017 at which Kevin Esvelt is the keynote speaker. More about this event after the 17th.
