Buttons and threads, or how to achieve criticality in a non-linear fashion

I learned something a long, long time ago, first in studying the origin of life, and then in studying the relationships within networks of genes, and now when thinking about basic epidemiology. Nothing is linear. It’s an idea that’s been discussed since at least the 1980s, when Stuart Kauffman applied it to the logic of the emergence of life on Earth. Here he is talking about the appearance of autocatalytic sets, that is, collections of interlinked enzymes (or ribozymes) that generate emergent properties, like a metabolism.

Now, the next question is how hard is it to get such systems? Does it take a careful crafting of a chemist, or can it arise by chance? The body of theory I’ve been working on now for more than a decade suggests that it’s not hard.

You see this with an analogy: suppose you take 10,000 buttons and spread them out on a hardwood floor. You have a large spool of red thread. Now, what you do is you pick up a random pair of buttons and you tie them together with a piece of red thread. Put them down and pick up another random pair of buttons and tie them together with a red thread, and you just keep doing this. Every now and then lift up a button and see how many buttons you’ve lifted with your first button. A connective cluster of buttons is called a cluster or a component. When you have 10,000 buttons and only a few threads that tie them together, most of the times you’d pick up a button you’ll pick up a single button.

As the ratio of threads to buttons increases, you’re going to start to get larger clusters, three or four buttons tied together; then larger and larger clusters. At some point, you will have a number of intermediate clusters, and when you add a few more threads, you’ll have linked up the intermediate-sized clusters into one giant cluster.

So that if you plot on an axis, the ratio of threads to buttons: 10,000 buttons and no threads; 10,000 buttons and 5,000 threads; and so on, you’ll get a curve that is flat, and then all of a sudden it shoots up when you get this giant cluster. This steep curve is in fact evidence of a phase transition.

If there were an infinite number of threads and an infinite number of buttons and one just tuned the ratios, this would be a step function; it would come up in a sudden jump. So it’s a phase transition like ice freezing.

Now, the image you should take away from this is if you connect enough buttons all of a sudden they all go connected. To think about the origin of life, we have to think about the same thing.

The pattern should also affect how we think about genes. We’ve got about 20,000 genes; each gene influences the expression of some set of other genes. You may think you know exactly which genes are directly affected by a gene you are interested in — you can do experiments and work out the connections, a process called epistasis — but because each of those genes also have multiple connections, you in effect have to consider that every single gene in some way influences the activity of every other gene. Tug on one, and every other gene in the system is affected. Each of us is a supercluster of interacting genes, being tugged on in various ways by the environment.

I’m not an epidemiologist, but this also how I think about the pandemic. I am a button. I’ve been alone for months; if I had gotten the disease, I would have suffered alone but I’d also have been a dead-end for the virus. Now my wife is home, another button, and we are tied together with a red thread such that if I get the disease, she almost certainly will, and vice versa. But also, she was living with my daughter, her husband, and my granddaughter for a few months, she was part of a four-button cluster, which I’ve now joined. If one of us had the virus, it would have readily spread within that group. But it would have ended there.

Unless…what if I cheated? I decided to go out to a bar and chat with ten friends. I’ve basically connected a red thread to each of their clusters, and increased my connectivity greatly. Maybe you think it’s still a manageable number, but that’s only because you don’t see all the red threads outside of your immediate group. The point of Kauffman’s analogy is that the expansion of the network is not linear, as you might naively expect, but jumps rapidly as the number of connections increases, and can undergo a phase transition, where just going out to a bar can achieve criticality, and suddenly you are connected to everyone in the country, and the virus has avenues to reach everyone.

So think of yourself as a button. Every time you touch someone, lean in close and breathe their air, you are tying a red thread to them, linking your fate to some degree to them. You can safely build a little network with close family, and you’re still OK — the threads tangle together just your small family unit. But if your child has a playdate with a neighbor’s kid…they have made a new thread that encompasses everyone in your family, and everyone in the neighbor’s family, and you’ll have no idea how many threads connect you all. And if you decide to take the whole family to that newly opened beach and mingle with thousands of other people, forget about it — the number of connections have shot up exponentially. You’ve lost all control.

The problem is that people don’t grasp the idea of exponential increases intuitively. I don’t. I’ve worked with enough models that I know that these kind of phenomena can produce surprisingly large effects rapidly, though, and that our current situation is a perfect example of that kind of phenomenon, and damn, stay home and stop stitching all those buttons together.

Back to the spider grind

I took a tour of my house this morning to see how the spiders were shaping up. I found lots, even more than I did last week. Some were familiar, like Attulus fasciger, who had captured a mosquito-like creature. Good work, young lady!

Of course there were lots of Salticus scenicus around.

The exciting but somewhat disappointing discovery was that Parasteatoda abounded — they’d colonized several inset corners of the house and areas around the downspouts, where they had good cover and great places to hide.

The disappointing part was my own failure: I couldn’t get a good picture of any of them! They were all living in little houses made of plant debris, and if I tapped on them to ask them to come out, they did a typical Parasteatoda thing: they’d immediately bungee straight down to the ground. They’re conveniently predictable when trying to catch them, but I just wanted to say hello and take a picture.
To see what I mean about the difficulty, I saved one photo of one tucked into a bit of dried flower petal, with just her blurry butt sticking out.

I’ve got 4 of these spider nests tagged now, and I’ll be back tomorrow and will try to get some better pictures. Except I think we’ve got thunderstorms predicted for Sunday…so maybe a little later.

You can see the photos, if you really want to, on Patreon or Instagram, as usual.

We’re all going to come out of this with new phobias

I’m starting to think I never want to be around people again, what with all their filthy, moist exhalations.

On the plus side, I’ve always wanted an excuse to wear a mask and cover this homely face. I look forward to the new support for industries that make fashionable face wear — I would like a formal mask for special occasions, a professional mask for work, and a wild & crazy mask for partying in the streets (alone, of course). I may also need a spider mask for those days I’m focused on arachnids, even though they tend not to sneeze.

Modern comic book history, in 3 minutes

As a person who mostly skipped any engagement with comic books in the 80s and 90s (my sons got into them a bit during that period), this short video seems to perfectly encapsulate my experience with them. Rob Liefeld and Todd McFarlane are shown creating a new superhero character while Stan Lee kibitzes. The amazing thing is how Lee zeroes in on the deficiencies of their creation — all flash and glitz, no story and no character — and closes with words of prophecy.

“The kids like it!”

Playing catch-up for a bit

After our long, long drive yesterday, I thought this would be a good day to rest and recover. I forgot that I’d brought Mary home. She was out in the garage at 7:30 fueling and oiling the lawn mower, eager to get to work cutting grass. I was not. I have more sedate plans.

  • I was up at 6 tinkering with computers. I’ve mentioned before that my Mac is on its last legs, with keys falling out and mysterious errors cropping up now and then, but the price of replacing it was prohibitive, especially since my disposable income, which wasn’t much to begin with, is flowing outwards to deal with legal debt. After a few days in my daughter’s Reality Distortion Field, in which she pointed out that I could get a high-end Linux machine for a thousand bucks less than my Mac upgrade, I decided to tinker. I installed the free Pop!_OS on an old Windows machine that I found intolerable — Windows is an ugly abomination — and brought it back to life. I’m going to work with it for a while to see if my old brain can readjust itself to use Unix instead of the MacOS, which I hate to say has become increasingly ugly over the years. I despise iTunes almost as much as I do Windows.

  • I’m going to spend some time in the lab this morning giving loving attention to my spiders, who have been neglected now for almost a week. Baby want a snackums? I have some nice flies for you.

  • I will obey my mistress after the spiders are made content. She has assigned me the task of cleaning out and sterilizing the car we spent 14 hours in yesterday. This may require fire.

  • I’ve got this working Raspberry Pi with a NOIR camera that we had set up to take pictures, and I’ve got this spider cage here at home, and now I have to figure out how to mount the camera above it at a reasonable distance that encompasses the whole field of view with reasonable resolution. Alternatively, I may have to build a dedicated cage of smaller size that will compromised between freedom of movement for the spider and adequate field dimensions for this camera. I’m thinking ring stands, tripods, hot glue, and popsicle sticks, because I’m focused on cheap and easy.

  • Mary has been looking at this bachelor pad I’ve been occupying with a glint in her eye. Who knows what she’ll order me to do next?

  • I’ve got some weekend cooking to do. I’ve been frustrated by the lack of garam masala in Morris, so I’d ordered a bunch of it online. Yes, I have a 5 lb bag of garam masala now, in case anyone needs to borrow a cup of it. I hope Mary likes curry.