Overweening Generalist

Friday, May 20, 2016

Synthetic Biology and Giambattista Vico

Less than two months ago as I write this, J. Craig Venter and his team published in Science the deets on how they built a synthetic organism, called "Syn3.0," and it's got only 473 genes. This is the lowest number of genes that we know of for a self-replicating living thing that doesn't require a host.

It's a sober-seeming Frankenstein scene, is it not?

HERE is a nice write-up in Nature on this

They did this via trial and error; they didn't build Syn3.0 from scratch. They took a bacterium, Mycoplasma mycoides, which lives in cattle, and painstakingly and systematically knocked out genes to see if they were truly essential. If a gene seemed to be essential for life, or a gene played a critical role in the regulation of other genes, they left it in. They whittled away a lot.

A complex bacterium like E. coli has around 6000 genes; humans have around 19,500.

What appears most fascinating to Venter and his crew (and me too) is this: once they finished and confirmed they had synthesized/whittled away a new organism, they still couldn't figure out exactly what 149 of the 473 genes did that were so essential to life. So: we don't know 1/3 of what is essential to life. We have our work cut out for us...or these synthetic biologists/fancy bio-hackers do.

The rest of us, like the girl who just ate a slice of pizza with anchovies, wait with baited breath.

This highlights how much we don't know, and makes ever-clearer the reason why, after Venter and scientists working for the Unistat government "mapped" the human genome 13-16 years ago, miracle breakthroughs in health and medicine did not pour forth immediately after.

                                              a human-made bacterium, believe it or not
A Variation on a Theme
My favorite analogous explanation for this went something like: for hundreds of years we heard wonderful music but weren't sure where it was coming from. Through a Herculean effort by legions of biologists, eventually we learned that this music had the structure of something we discovered was a "piano." Tremendous efforts by public sector genius and private wizards finally produced a map of the music: a Steinway piano! What a fantastic discovery of human ingenuity!

But then: you need to learn how to play Beethoven. Just having the piano and knowing that you press certain keys little hammers inside struck strings and made "notes"? Not good enough. We had to actually understand the thing. We had to learn how to play something like the Appassionata

Tall order? Of course! Would we shrink from it and ditch our lessons and not practice our Hanon exercises? No. We're all in. Here's where Vico makes his entrance...

Expository Material
Giambattista Vico (1668-1744), an early admirer of Descartes, later did a 180 from "Renato" (as Vico refers to him in his Autobiography) and said no: it's not correct that we humans can only truly have knowledge of the physical world because we can apply our rationality and math to understand it; Renato said we can't know the human past, so forget about it. Vico said, anzi, we can only truly know what we have ourselves made: the social world. Law, politics, art, history, etc. Even mathematics is a human construction. We did not make Nature, so we can't truly know it. Scholars of Vico (who call themselves Vichians and not Viconians) refer to this idea as Vico's principle of verum factum

Because of verum factum, various scholars have called Vico the first Anthropologist, the inventor of the sociology of knowledge, the first great modern sociologist, etc. It's interesting. I don't know what to think, because Vico's writing - especially in his magnum opus The New Science - seems to alternate between staggeringly prescient ideas and really crazy and "wrong" ones. Here is one of his most famous passages, and the one cited most often with regard to verum factum:

Still, in the dense and dark night which envelopes remotest antiquity, there shines an eternal and inextinguishable light. It is a truth which cannot be doubted: The civil world is certainly the creation of humankind. And consequently, the principles of the civil world can and must be discovered within the modifications of the human mind. If we reflect on this, we can only wonder why all the philosophers have so earnestly pursued a knowledge of the world of nature, which only God can know as its creator, while they neglected to study the world of nations, or civil world, which people can in fact know because they created it. The cause of this paradox is that infirmity of the human mind noted in Axiom 63. Because it is buried deep within the body, the human mind naturally tends to notice what is corporeal, and must make a great and laborious effort to understand itself, just as the eye sees all external objects, but needs a mirror to see itself. - section 331, translation by Dave Marsh

A couple of notes:
- The Inquisition was very strong in Naples, when Vico was doing his thing. The reference to "God" in his text is problematic, to my eyes. Perhaps he truly believed all the things he says about "God," but I see plenty of room for doubt. In his Autobiography he certainly seems to have been heavily influenced by Lucretius, who popularized Epicurus. Vico also has plenty of oblique things to say about the deep and enduring history of class warfare and he doesn't seem all that admiring of history's aristocracy. Vico was one of those thinkers who seemed to have read everything available; he had personally known thinkers around Naples who had paid for speaking out for thought free of Church restrictions. He certainly had read about others who'd suffered at the hands of the Inquisition.

-Hobbes and many other thinkers of antiquity and the Renaissance had ideas like verum factum, but they only mentioned this notion in passing; with Vico this idea is central to his thought.

-Axiom 63 reads thus:
Because of the senses, the human mind naturally tends to view itself externally in the body, and it is only with great difficulty that it can understand itself by means of reflection. This axiom offers us this universal principle of etymology in all languages: words are transferred from physical objects and their properties to signify what is conceptual and spiritual. 

Finally: OG's Point, If Indeed He Has One?
When I first delved into Vico I thought verum factum was wrong: the revolution in modern science since the Renaissance was based on a special way of looking into nature: some phenomenon needed to be explained, hypotheses competed until a line of very fecund thought - a theory - led to a cascade of knowledge about the physical world. Ideas were freely exchanged and published and the idea that my experiment, while exciting, needed to be replicated by many others working independently for it to be considered "true"...this seemed to me like a vast leap in human knowledge. At the same time, the idea of "knowledge" in the Humanities (which to this day I love with a very deep passion) was not making gigantic strides. When scientific knowledge cashed out into Technology, which accelerated the human world, I just thought Vico, while exceedingly erudite and weird and entertaining, was a bit daft here.

Later, when reading people like Popper, Kuhn, Feyerabend, Foucault and Latour, I realized the physical sciences didn't actually work as neatly as I'd been led to believe. Further, the most successful physical theory ever - the quantum theory - led to philosophical quagmires dizzying and surreal. Did we really understand the physical world, or did we pragmatically go with what worked, while retroactively explaining what was "really" going on?

                                          Richard Feynman's blackboard at CalTech                           

Apocalypse and/or Utopia
Now, we are making living things. I'm quite sure Syn3.0 is merely the first of thousands of human-made living things. And Venter and his colleagues are playing Creator in order to understand, at a fine-grain level, the physical, chemical and biological way something does its thing.

Is verum factum then a "dead" idea? I don't know, but when Venter and his guys came up with an artificial living thing a few years ago, it prompted Obama to issue a bioethics review and the Vatican challenged Venter on his claim of creating life. And so has it ever been...

Finally: if you read the link to the article in Nature, you may have noted that Venter and his crew inserted their own names - literally - into the deep structure of Syn3.0. Why? As watermarks, a way of marking this territory of Life as human-made. They also inserted some quotes and one was from Richard Feynman's blackboard, as seen in the photo above: "What I cannot create I do not understand."

Sounds a lot like Vico to me.

"In Newly-Created Life Form, a Major Mystery," by Emily Singer

"Scientists Synthesize the Shortest Known Genome Necessary For Life," by Amina Khan

"Why Would Scientists Want to Build a Human Genome From Scratch?", by Sally Adee

The New Science, by Giambattista Vico, translated by Dave Marsh



Eric Wagner said...

Today we had a jeans day at my high school. Just saying.

In 2014 I practiced my Hanon exercises regularly for a short while.

I wonder what Vico would make of Trump. I wonder if Trump will rename July after himself. Interesting that the scientists added graffiti to their creation. Hip hop lives!

Great piece.

michael said...

Eric: that's a different study of jeans/genes: It's called jeaneology.

I found that the desire for serious technique has to be approached 6 days of the week, with a total committment and a metronome.

I'm already expecting Czar Donny to try some sorta Beer Hall Putsch if he's losing to the Iron Lady.

Thanks for the choice vibes, daddy-o!

Wes said...

Really enjoyed this piece, as usual.

michael said...

Wes: Thanks! I write with no remuneration, only hoping there are readers like you who are actually as interested in this stuff as I am.

(I also write to learn and to find out what I think I "know" about something, which is always a more mysterious process than it sounds.)

I'll keep going then!

Eric Wagner said...

I don't think I've ever committed to serious technique except as a poet. I do think one can commit to serious technique in a variety of ways.

michael said...

@Eric: I know there are various ways to improve technique on a musical instrument, but they all seem of a kind to me. (I've been playing/teaching for 35 yrs.)

With poetry/writing and I'd guess painting and acting and other artistic endeavors: yea, the techniques must be different.

I'm not sure if this was what you were getting at?

Eric Wagner said...

Michael, I think people develop a variety of sorts of technique on musical instruments. Some do it in different ways. I think Thelonious Monk, Dee Dee Ramone, Glenn Gould, Phil Lesh, Jay Z, and John Lennon, etc., developed their musical skills in very different ways.

I know hard work can accomplish things, but I think one can accomplish things in other ways as well. I remember a cartoon that said something like, "The left will never work for revolt because the left will never revolt against work." In Schoedinger's Cat the narrator says that people like to see evolution [or music] as a Promethean struggle, but one merely has to cooperate with the genetic code. Following Quantum Psychology, I think of it as cooperating with the morphogenetic fields.

On July 23, 1985, I visited Ingolstadt, Bavaria. The next day I visited the concentration camp at Dachau. When I saw the sign "Arbeit Macht Frei," I had a sense of my life purpose as unlearning the notion that work will set one free.

michael said...

@Eric Wagner: Oh, we're talking about "technique" and should have extensionalized it a bit: I agree with you about the semantic sense you seem to be using for "technique,": i.e., probably the most organic way to accomplish coherent musical self-expression is just via lots of playing. Dee Dee Ramone would never be in the discussion about technique in my semantic sense: extra-ordinary speed, dexterity, and sophistication with one's axe.

Monk was self-taught, but always seemed to be playing/jamming/gigging. No way Gould achieved that facility without lots of solitary woodshedding. I don't think of Lennon or Jay-Z in my semantic sense at all.

To clarify: My own musical esthetics do not require virtuosity, but I do love Paganini, Liszt, Coltrane, Allan Holdsworth, and John Petrucci for their wizardry in service to expression. Most of the music I listen to for the sheer joy of it does NOT feature chops on the order of Art Tatum, "Flight of the Bumblebee," or the Transcendental Etudes.