☞ Archaeology of Biology and Software

Technology, biology, and humility

Biology and technology are accreted messes.

As part of my book writing process, I was recently taking a look at Gregory Chaitin’s short book Proving Darwin. I found this point he made about biology and software and archaeology intriguing:

In fact, it’s like archeology—that’s what biology really is, a kind of software archeology! So there is artificial software, computer programs, and there is natural software, DNA. Nature invented software before we did, long before. And the origin of life is really the origin of software, the origin of DNA, a universal programming language found in every cell. A powerful programming language, one that can presumably express any possible algorithm, any set of instructions for building and running an organism. It is a programming language that we are beginning to understand, a very complicated programming language, one that has grown by accretion over the millennia…

While we are increasingly understanding the massively nondeterministic and complex nature of biology (cf. Philip Ball’s How Life Works) and I don’t want to make too much of the software comparison here, I appreciate the idea of exploring a technology—computational or biological—and seeing the deep history contained within it. For technological and biological evolution have proceeded slowly and iteratively over time, accreting changes. To quote Chaitin again, “As Jacques Monod said, Nature is a bricoleur, a handyman, a tinkerer. You make do with old things, you patch them up, you fix them so you can reuse them.”

This accretion resonated with an essay I wrote nearly a decade ago titled “Why Our Genome and Technology Are Both Riddled With ‘Crawling Horrors.’” A taste:

It’s hard to change these technologies that grow slowly and becoming increasingly messy. The people who initially designed them might be long retired, or even dead. Replacing the systems entirely demands a big upfront cost and comes with the risk of unmitigated failure. So we tinker at the edges of these kluges, treading carefully. When messy enough, these systems are sometimes even referred to as crawling horrors, in homage to the unspeakable monsters that haunt H.P. Lovecraft’s stories.

If this sounds vaguely biological, you are onto something. Many of the most important sequences of DNA in a human cell, such as the ones that power how our genetic code is translated or how we use energy, are the same ones that other, far different, organisms—separated by eons of time—also use. Essentially, this is the legacy code of biology. Sometimes these sequences remain unmodified, but often, through evolutionary time, these systems are also tinkered with, and changed.

In both of these realms, we can only understand these systems when taking an archaeological approach to them.

A corollary is that when we are dealing with complex organisms, we must also proceed with humility in understanding them. So instead of biohacking hubris, we should instead proceed this way (from another essay of mine):

When it comes to biology and nutrition, while there is no doubt so much more to learn (and not everything that stands the test of time is necessarily correct), an incremental tinkering approach, tempered by a lot of humility, might be much more effective in the long term than the quick fixes of biohacking.

Or we can at least recognize this:

xkcd: DNA

Technological and biology archaeology is needed for improved understanding of these systems. And so is humility. ■

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More on Maxis 2.0

Thank you so much to everyone who reached out to me about my idea about “Maxis 2.0.” It seems as if there is a lot of interest in this idea.

I also had a chance to speak with Chaim Gingold, author of Building SimCity, on The Orthogonal Bet podcast series where I poked a bit at the possibility of a Maxis 2.0.

One additional point I’d like to share is that I think there is also a clear need for a “HyperCard for simulation” (where you could build any SimCity you want, for example, based on your own ideas around urban dynamics).

This kind of idea is also noted in Ken Forbus’s amazing essay “Why computer modeling should become a popular hobby”:

Customizable simulations. Most simulations allow you to only change a handful of parameters over a narrow range. Simulations that make it easy to explore the consequences of major model changes, such as plugging in a different traffic model in SimCity 2000, enable more people to get "under the hood" and experiment in ways they find meaningful.

Perhaps this could be one of the first software applications released by a Maxis 2.0?

And by the way, perhaps a Maxis 2.0 could take as its inspiration some of the innovation around institutional forms that has been happening in non-traditional research organizations, considering that there is a lot of similarities here with what a Maxis 2.0 might need to do: R&D and interdisciplinary thinking at the intersection of simulation, gaming, complexity science, education, and engagement with the public.

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The Enchanted Systems Roundup

Here are some links worth checking out that touch on the complex systems of our world (both built and natural):

🜸 From boiling lead and black art: An essay on the history of mathematical typography: “Knuth was certain that it was time to help typography leap over phototypesetting—from matrices of hot lead to pages of pixels.”

🝳 How generative AI could reinvent what it means to play: “AI-powered NPCs that don’t need a script could make games—and other worlds—deeply immersive.”

🝤 Life Secrets of the Late Bloomers: “Being an ugly duckling in your youth can be the key to becoming a successful swan later in life”

🜹 A Lego CNC Pixel Art Generator

🝊 Computational Life: How Well-formed, Self-replicating Programs Emerge from Simple Interaction: “We show that when random, non self-replicating programs are placed in an environment lacking any explicit fitness landscape, self-replicators tend to arise. We demonstrate how this occurs due to random interactions and self-modification, and can happen with and without background random mutations.”

🜸 The Rubik’s Cube Turns 50: “Mathematicians and hobbyists have had a half-century of fun exploring the some 43 billion billion permutations of Erno Rubik’s creation.”

🝖 When RAND Made Magic in Santa Monica: “RAND’s halcyon days lasted two decades, during which the corporation produced some of the most influential developments in science and American foreign policy. So how did it become just another think tank?”

🝊 Samuel Newman's Concordance, and How "Delve" Changed the World: ‘How the word "delve" is channeling the past to talk to the present, and the future.’

🝳 BusyBeaver(5) is now known to be 47,176,870

Until next time.