Emergence and the pandemic

I love this video. I also found very helpful an article in The Economist, Anatomy of a killer, that gives a basic introduction to the biology. [Unfortunately, it is behind a pay-wall. I subscribe to the hard copy, which I highly recommend.]. The New York Times also has a helpful tutorial How coronavirus hijacks your cells.

So what do a new virus, an epidemic, social distancing, and panic buying have in common?

They are all examples of emergent phenomena as they all have three particular properties.

First, each phenomenon involves a system with many interacting components.

Second, the system possesses a property, an ability to exhibit a specific phenomenon, that the individual components of the system do not have.

Third, the phenomenon is hard to predict, even with a knowledge of the details of the system components and of the interactions between the different components.

Consider the four examples I gave.

An epidemic arises when a few people are infected with a virus who in turn infect others who infect more people until a significant fraction of the whole population is infected. With a single human or even a few, the concept of an epidemic does not make sense.

Even though we do know a lot about epidemiology it's very hard to predict the scale of an epidemic and to decide on the most effective measures to ``flatten the curve.’’

Associated with epidemics there are emergent concepts such as tipping points (R0 larger than 1), super spreaders, and herd immunity [Scott Page gives a nice 9 minute lecture on this].

The concept of panic buying does not make sense if there is only a single customer. The phenomenon arises not just from the actions of one shopper or even a group of shoppers. Individual shoppers in a store don’t just interact with each other in a single shop but also interact with their social and informational networks.  Who would have predicted that we would see such silly things as panic buying of toilet paper?

Many of us had not heard of social distancing until this year. At first, you might think that social distancing is just something that arises from a government regulation, i.e., it is  ``top-down ‘’ rather than ``bottom-up’’. However, it occurs as a result of interaction between all the individuals in the society and with scientific advisors and then the government, but this does not mean that they will and we do see this in certain countries certain cultures and in certain demographics even though

If the government ordains social distancing, it does not mean it is practiced. Certain cultures and demographics will not follow government edicts. Rather, society self-organises to produce social distancing. Some people practice it, voluntarily or in response to a government edict, others see them doing it and then they follow. You can go to the park and you see people only talking in pairs and more than two metres apart and so then you're more likely to practice it.

 SARS-CoV-2 is a new virus. As far as we are aware it did not exist previously in humans. New viruses emerge through evolution. [There is a nice video from Stated Clearly ] 

Coronaviruses are common in animals and can gradually mutate in interaction with their environment. At some point this virus crossed the species barrier to humans; it is still adapting to its environment. There are many components of the system; the individual viruses don't interact with each other but with their environments.

A single virus also has emergent properties (its ability to infect specific cells, reproduce itself, and to survive inside a water droplet). Central to a single SARS-CoV-2 virus particle is an RNA molecule with about 30,000 base pairs.  All of those together provide the genetic information that is used to reproduce. Having the individual base pairs, or a subset of them, or the RNA without the six

proteins and membrane.  Knowing all the genetic information is useful but cannot necessarily be used to predict the structure of the virus, its function, or how to develop a vaccine.

Why does an emergent perspective matter? 

From a purely scientific point of view, there are many interesting and fascinating phenomena that would be nice to understand, from the biochemistry of a single virus to the spread of the virus by international travel. If we understand these phenomena better, particularly at all the different scales discussed below, then we have a better chance of taking effective action to stop the spread of the virus, whether it is as individuals washing their hands, practicing social distancing, government policies, or development of vaccines.

There are many scales to the pandemic problem: length scales, time scales, and number scales.

The distance scales cover a range of about 15 orders of magnitude.

A single virus particle is about 10 nanometers in diameter (10^-8 m). A cell in the human respiratory tract is about 100 times larger.

Then we can keep on going up to 10,000 km (10^7 m), the distance that some people flew to carry the virus around the world.

The range of timescales is from microseconds (?) for a single virus particle to attach itself to a human cell, up to several hours to produce thousands of copies of the virus inside that cell, to the weeks for infected individuals to develop symptoms, to the time for new government policies to take effect.

And, the time scales many are particularly interested in: how long we will be in self-isolation? how long until the economy ``recovers''?

The numbers range from reproduction numbers for a single virus in a single cell, numbers infected from a single human to the millions of people infected, to the trillions of cells in a human body.

There is a stratification of reality or hierarchy associated with these different scales to length, time, and number.

RNA, Virus, Cell, immune system, organs, individual human, individual’s (physical) social contacts, city, country.

An emergent perspective is helpful in at least three ways.

First, it highlights the limitations of reductionism. Even if we know the details of the individual components of a system and how they interact with each other that does not necessarily mean we have an understanding of the properties of the whole system. For example, we already know the nucleic acid sequence of the RNA for SARS-CoV-2, the associated genes, and the physical structure of a single virus particle, including its six proteins.

This is helpful and wonderful. However, it does mean we really understand the virus, including how to develop a vaccine. Knowing the genome does not enable the prediction of the structure of the virus.  This is similar to the problem of predicting a protein structure from a knowledge of its amino acid sequence.

In biology there is a helpful and common paradigm: structure determines property which determines function. This is why there is so much emphasis on protein structure determination.

But knowing the structure does not always enable us to predict the property and particularly the function. Function is an emergent property.

Second, an emergent perspective highlights the tension between universality and particularity.

For example, COVID-19 is one of the hundreds in the coronavirus family. They have quite similar structures and properties. But this coronavirus is very particular in a devastating way. Small changes in the genetic code or proteins could make it even more dangerous, or impotent. 

Thirdly, an emergent perspective highlights the significance of the stratification of reality. At each stratum there are unique entities, phenomena, concepts, techniques, and theories. This is the origin of different scientific disciplines.

Observing phenomena at one stratum does not reveal what is going on at a lower stratum.
This is what Laughlin and Pines call the ``protectorate''. 

This applies whether considering a single RNA molecule, a virus particle, a respiratory cell, or groups of shoppers.

Panic buying is unique to the stratum of groups of consumers. The underlying causes from the psychology of individuals and groups are hidden.

Studies of consumer behaviour provide no insights for immunology and visa versa.

A pandemic and its aftermath is a wicked problem: it is complex and difficult to solve.

There is some intellectual beauty in the multi-disciplinarity of the problem; it involves biochemistry, cell biology, immunology, medicine, public health, sociology, psychology, politics, economics, and mathematical modeling. It does not even end there as the humanities come in to play. Responses to the crisis, from individuals to governments, involve fundamental philosophical and theological questions about ethics, values, meaning and purpose, suffering and death.