Some principles of network epidemiology

Lockdowns and “flattening the curve” are very much in the news right now, so I thought it was timely to post about some principles of network epidemiology. The charts below (click to zoom) show the simulated spread of a disease (in a small “toy” population of 2000) subject to certain assumptions. The blue lines show the total number of cases over time (adding up those infected, recovered, and dead). This total number is important because some percentage of the final total will die, and we want to minimise that (if we can). The red lines show the number of current infections over time. This is important because some percentage of the red numbers are in hospital, and the red peak therefore represents peak load on the medical system.

In the top row, we have connections happening at random, with increasing social distancing happening from left to right. Moderate social distancing doesn’t change the fact that almost everybody gets the disease, but it does delay and reduce the peak, thus taking strain off the medical system. Extreme social distancing saves many lives, but only if social distancing is continued for a long time (in real terms, until a vaccine is available, which is almost certainly not sustainable).

In the middle row, we have the same number of contacts happening as in the top row, but most of the contacts are within limited social circles. Such contacts, between family members and close friends, are less serious than contacts with strangers. If Peter is your close friend, and you catch the virus, then there’s a reasonable chance that Peter caught it the same way, and so there’s a reasonable chance that your contact with Peter makes no actual difference. If Peter is a spouse, child, or flatmate, that’s quite a good chance. Contacts with strangers, however, can spread the disease from one social circle to another, and so are far more serious.

In the bottom row, we again have the same total number of contacts happening, but a few “super spreaders” have many more contacts than average (while the majority have slightly less than average, to compensate). This third scenario is significantly worse than the top row – higher, earlier, red peaks, and many deaths even when there is extreme social distancing. Unfortunately, experience has shown that medical personnel, in spite of the fantastic work that they do, have the potential to be serious “super spreaders,” because:

  • they have contact with many patients;
  • the patients are strangers; and
  • the patients are more likely than average to be elderly and/or vulnerable.

This is why personal protective equipment (PPE) for medical personnel is so critically important, as are good testing protocols for medical personnel. Other kinds of “super spreaders” also occur, of course, and it is important to identify them, test them, and provide them PPE (or stop them doing what they’re doing, if it’s non-essential – some jurisdictions with supposedly strict rules are still allowing prostitutes to operate, for example).

Overall, if we look at columns in the picture (all three charts in each column have the same total number of contacts), we see that the kind of contact is just as important as the number of contacts. Isolation regulations in some jurisdictions don’t always recognise that fact, unfortunately.


The Lost World by Michael Crichton: a book review


The Lost World, by Michael Crichton (1995)

Recently, because this is the season for extra reading, I re-read The Lost World by Michael Crichton (which was made into a 1997 film). This novel turns 25 years old in September. Its main plot needs no explanation, of course. Just like Jurassic Park, there’s action, there’s excitement, and there’s dinosaurs chasing people.

As with all Crichton novels, there are technical and scientific themes that do not make it into the film. I had forgotten, for example, that the original mobile laboratory is solar powered: “He wants them light, I build them light. He wants them strong, I build them strong – light and strong both, why not, it’s just impossible, what he’s asking for, but with enough titanium and honeycarbon composite, we’re doing it anyway. He wants it off petroleum base, and off the grid, and we do that too. … The Explorer with the black photovoltaic panels on the roof and hood, the inside crammed with glowing electronic equipment. Just looking at the Explorer gave them a sense of adventure…” (pages 64 & 94)


Velociraptor skeletal cast at the Dinosaur Journey museum in Colorado (original photo by Jens Lallensack)

Another theme, naturally, is the changing scientific view of dinosaurs, and indeed other things, over time (in fact, the book and film are already out-of-date in some respects): “Back in the 1840s, when Richard Owen first described giant bones in England, he named them Dinosauria: terrible lizards. That was still the most accurate description of these creatures, Malcolm thought. … the Victorians made them fat, lethargic, and dumb – big dopes from the past. This perception was elaborated, so that by the early twentieth century, dinosaurs had become so weak that they could not support their own weight. … That view didn’t change until the 1960s, when a few renegade scientists, led by John Ostrom, began to imagine quick, agile, hotblooded dinosaurs. Because these scientists had the temerity to question dogma, they were brutally criticized for years, … But in the last decade, a growing interest in social behavior had led to still another view. Dinosaurs were now seen as caring creatures, living in groups, raising their little babies.” (page 83)


Tortuga Islands, Costa Rica (original photo by “rigocr”) – is this the mysterious Isla Sorna?

As with many Crichton novels, scientific hubris is a major theme. Other themes include the education of children (both dinosaur children and human children), information systems design, the theories of Stuart Kauffman about self-organisation and evolution, and the importance of what is now called the complex systems view.

Overall, this is a good solid action novel, with several scientific and philosophical themes to think about. Goodreads rates it 3.78. I’m giving it only 3½ stars, in part because it’s a little too much like Jurassic Park. But it’s certainly well worth a read.


The Lost World, by Michael Crichton: 3½ stars


Topic Analysis on the New Testament

I have been experimenting recently with Latent Dirichlet allocation for automatic determination of topics in documents. This is a popular technique, although it works better for some kinds of document than for others. Above (click to zoom) is a topic matrix for the Greek New Testament (using the stemmed 1904 Nestle text, removing 47 common words before analysis, and specifying 14 as the number of topics in advance). The size of the coloured dots in the matrix shows the degree to which a given topic can be found in a given book. The topics (and the most important words associated with them) are:

A better set of topics can probably be obtained with a bit more experimentation. Alternatively, here (as a simpler form of analysis) are the relative frequencies of some Greek words or sets of words, scaled to the range 0 to 1 for each word set (with the bar chart showing the total number of words in each New Testament book). Not surprisingly, angels appear more frequently in Revelation than anywhere else, while love is particularly frequent in 1 John:


Triboelectricity

The triboelectric effect was discovered 2600 years ago by Thales of Miletus. When items in this illustrated (incomplete) list are rubbed together, the low-numbered item gains a positive charge, and the high-numbered item gains a negative charge.

For example, glass rubbed with silk (or, even better, polyester) gains a positive charge, once called “vitreous electricity.” Amber rubbed with wool gains a negative charge, once called “resinous electricity.” Indeed, our word “electron” comes from the Greek ἤλεκτρον, meaning “amber.”


Chemistry can be beautiful: the classic flame test

The flame test occasionally comes up in classic detective fiction: “He snapped off the lights, and we were left with only the sodium flame. In that green, sick glare a face floated close to mine – a corpse-face – livid, waxen, stamped with decay…” (Dorothy L. Sayers & Robert Eustace, The Documents in the Case)

Spectral lines in the image are taken from Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2019). NIST Atomic Spectra Database (ver. 5.7.1), [Online]. National Institute of Standards and Technology, Gaithersburg, MD. Photographs in the image are public domain, from Wikimedia Commons.


Dune by Frank Herbert: a book review


Dune by Frank Herbert (1965)

I recently re-read the classic 1965 novel Dune by Frank Herbert. This is Frank Herbert’s best book, and one of the best science fiction novels ever written. It won the Hugo Award in 1966 (jointly with Roger Zelazny’s This Immortal) and won the inaugural Nebula Award. It became a quite terrible 1984 film and a somewhat better miniseries.

Parts of the novel are reminiscent of the work of Cordwainer Smith, notably the idea of a desert planet producing spice, and the idea that navigating a faster-than-light ship requires a guild of unusual navigators who can see into the future. However, most of the novel was so original that it became a huge hit when it first appeared. Themes that are particularly notable are those of planetary ecology, intergalactic politics, and unusual human skills.

I have always been moved by Herbert’s idea of a symbolic ecological language that can “arm the mind to manipulate an entire landscape” (Appendix 1), and the idea of making ecological literacy a key part of education:

At a chalkboard against the far wall stood a woman in a yellow wraparound, a projecto-stylus in one hand. The board was filled with designs – circles, wedges and curves, snake tracks and squares, flowing arcs split by parallel lines. The woman pointed to the designs one after the other as fast as she could move the stylus, and the children chanted in rhythm with her moving hand.
Paul listened, hearing the voices grow dimmer behind as he moved deeper into the sietch with Harah.
‘Tree,’ the children chanted. ‘Tree, grass, dune, wind, mountain, hill, fire, lightning, rock, rocks, dust, sand, heat, shelter, heat, full, winter, cold, empty, erosion, summer, cavern, day, tension, moon, night, caprock, sandtide, slope, planting, binder. …’
” (Chapter 22)

The unusual ecology of the desert planet Arrakis encourages us, of course, to think more deeply about our own planet (and Arrakis was apparently inspired by the Oregon Dunes here on Earth).

Also fascinating is the idea that the human race has turned away from computers and the Internet, and gone back to training human minds to remember, calculate, and think:

‘Once men turned their thinking over to machines in the hope that this would set them free. But that only permitted other men with machines to enslave them.’
‘Thou shalt not make a machine in the likeness of a man’s mind,’ Paul quoted. […]
‘The Great Revolt took away a crutch,’ she said. ‘It forced human minds to develop. Schools were started to train human talents.’
” (Chapter 1)

The most obvious theme, and the source of the novel’s action, is the galaxy-wide intrigue between the noble House Corrino, House Atreides, and House Harkonnen; the resulting warfare between them; and the resistance of the desert Fremen to occupation (inspired by Lawrence of Arabia):

Paul took two deep breaths. ‘She said a thing.’ He closed his eyes, calling up the words, and when he spoke his voice unconsciously took on some of the old woman’s tone: ‘ “You, Paul Atreides, descendant of kings, son of a Duke, you must learn to rule. It’s something none of your ancestors learned”.’ Paul opened his eyes, said: ‘That made me angry and I said my father rules an entire planet. And she said, “He’s losing it.” And I said my father was getting a richer planet. And she said. “He’ll lose that one, too.” And I wanted to run and warn my father, but she said he’d already been warned – by you, by Mother, by many people.’” (Chapter 2)

Goodreads rates this classic science fiction novel 4.2. I’m giving it 4½ stars (but be aware that the sequels are not nearly as good).


Dune by Frank Herbert: 4½ stars


American Solar Challenge Late March Update

It is not much more than three months until the American Solar Challenge. Scrutineering begins on July 10th, assuming that the coronavirus pandemic doesn’t interfere.

Kansas (785) have finished their battery pack, Illini (22) have cancelled their car-reveal event [no image], as have Esteban (55), Michigan (2) have withdrawn from the event entirely (citing coronavirus reasons), and UBC (26) have made fantastic progress on their Daybreak.

See also my updated illustrated list of teams. At present we have 33 teams registered, but some teams are obviously in trouble, and some cars are not going to get built before July. On the other hand, other teams are making good progress. Nevertheless, the shadow of the coronavirus pandemic lies over the whole event.