Why Synthetic Protein Research Needs More Funding

From David Baker on Nautilus:

Even more remarkably, nature seems to have made use of only a tiny fraction of the potential protein structures available—and there are many. Therein lies an amazing set of opportunities to design novel proteins with unique structures: synthetic proteins that do not occur in nature, but are made from the same set of naturally-occurring amino acids. These synthetic proteins can be “manufactured” by harnessing the genetic machinery of living things, such as in bacteria given appropriate DNA that specify the desired amino acid sequence. The ability to create and explore such synthetic proteins with atomic level accuracy—which we have demonstrated—has the potential to unlock new areas of basic research and to create practical applications in a wide range of fields.

Alternatively: maybe nature only uses a fraction of the possible proteins for a reason — it has selected for the ones that work. Regardless, I believe research in fundamental biology is always a good idea.

Take protein logic systems, for example. The brain is a very energy-efficient logic system based entirely on proteins. Might it be possible to build a logic system—a computer—from synthetic proteins that would self-assemble and be both cheaper and more efficient than silicon logic systems? Naturally occurring protein switches are well studied, but building synthetic switches remains an unsolved challenge. Quite apart from bio-technology applications, understanding protein logic systems may have more fundamental results, such as clarifying how our brains make decisions or initiate processes.

DeLanda Destratified

De Landa Destratified on Techgnosis.

Some quotes I like:

I don’t believe there is such a thing as postmodernism. It’s exhausted. We truly need a complete new thing, and [Deleuze and Guattari’s] A Thousand Plateaus is the direction. Those guys are fifty or sixty years ahead of everyone else. You read it at first and you think you’re reading poetry: “Metals are the consciousness of the planet.” Get out of here, what the fuck is that? Then you read about metallic catalysts, how in a way they are like probing heads that unconsciously accelerate certain reactions and decelerate certain others. They allow the exploration of an abstract chemical space by probing and groping in the dark. And you realize those two are right.

Chris Langton at Los Alamos later set out to classify all possibly cellular automata – which basically means abstract spaces with many dimensions – depending on how many rules they have. He discovered that there’s a range, a magic region if you will, where your cellular automata game will develop all the unpredictable patterns that the Game of Life developed. If your rules are too rigid, nothing interesting will happen. If they are too loose, nothing interesting will happen. But if they are in the middle region – what they call the edge of chaos – all kinds of organizing processes will happen.

The metaphor they use is solid, liquid, gas. If the system is solid, too crystallized, its dynamics are completely uninteresting. If it’s gaseous, it’s also uninteresting – all you have to do is take averages of behavior and you know what’s going on. Liquids have a lot more potential, with all kinds of attractors and bifurcations. Now what they’re coming to believe is that the liquid state in nature – not just actual liquids, but liquidity in the abstract sense of being not too rigid or too loose – these liquid systems “poised on the edge of chaos” are natural computers.

One of the things that amazes me is that the Himalayas – which people think of as the paradigm of the stable – are still moving up one millimeter a year because India is still clashing with Central Asia. They’re a ripple in the surface of the Earth. We cannot conceive of a clash that would last millions of years – our time frame is too limited. Imagine an observer with a time-scale so large that he could see this clash. He wouldn’t even see us. Species to him would seem like vast amounts of bio-mass in constant change. He would see evolution. Everything that matters to evolution happens across millennia. That observer would see species mutating and flowing. He would probably worship flows – unlike us, who, because of our very, very tiny time-scale of observation, tend to worship rocks.

Psalm 78:35, “And they remembered that God was their rock, And the Most High God their Redeemer.” So yeah, I think DeLanda’s on to something.

I’m about half-way through DeLanda’s 1000 Years of Nonlinear History, I’ll post my notes when I’m done, but so far DeLanda’s thought is very interesting and very far ahead of most everyone else.

How much the culture of learning has changed

The bestselling novel of 1961 was Allen Drury’s Advise and Consent. Millions of people read this 690-page political novel. In 2016, the big sellers were coloring books.

Fifteen years ago, cable channels like TLC (the “L” stood for Learning), Bravo and the History Channel (the “History” stood for History) promised to add texture and information to the blighted TV landscape. Now these networks run shows about marrying people based on how well they kiss.

This is from Seth Godin, The Candy Diet.

Even if only a few people use precise words, employ thoughtful reasoning and ask difficult questions, it still forces those around them to catch up. It’s easy to imagine a slippery slope down, but there’s also the cultural ratchet, a positive function in which people race to learn more and understand more so they can keep up with those around them.

Turn the ratchet. We can lead our way back to curiosity, inquiry and discovery if we (just a few for now) measure the right things and refuse the easy option in favor of insisting on better.