Saturday, February 09, 2013

Bacteria Ain't Dumb


Dr. James Shapiro regaled us with stories tonight, of the picture biology has painted in the last 40 years, which, to read press accounts, has yet to be unveiled.  These aren't secrets though, just technical results that require some added vocabulary.  We were outside of the standard 4000 words or whatever English speakers tend to get by on.

The short of it is:  cells don't just change (morph) because hit by random cosmic rays, with natural selection then weeding out the losers.  There's no time to be that stupid and cells are not.  They form alliances, as symbiants, as parasites, as lethal adversaries or whatever, and they exchange DNA / RNA.  They seem to share information.

We went through some of the history.  Barbara McCormick's research is key.  Cells have lots of feedback loops and respond to stresses by moving DNA around.  Those sequences are not read-only, but read-write, and there's lots being encoded based on what's happening or what gets in.  Since Lynn Margulis we've started to get it:  once independent life forms have swallowed one another.  Today's mitochondria and chloroplasts where at one time bacteria in the wild.

The microbiology also seems to show that once X swallows Y, a redivision of labor occurs, with X taking on perhaps more of Y's responsibilities.  The eukaryotes have their own special ways of doing things etc.

If you think of cells as both cognisant and sentient, you'll have access to more of the English grammar needed to map the circuitry a little.  Fear of anthropomorphism is misplaced.  It's an intelligent mapping of an articulated part of language to something complex.  Letting British novelists describe intra-cellular relations using the the tropes and conventions of their trade might actually make for better cell biology, when it comes to conveying the nuances within our gray matter.  Make it more of an opera, and you'll get it.  It's Machiavellian all the way down.

It's when cells get starved that they really go crazy.  Being unsuccessful, or "insulted" as Terry put it during the Heathman dinner afterwards, is a primary stimulus.  As they said in est at the graduation, it's being losers that reactivates us, as humans (vs. the angels).  That's when we / they innovate, duplicating whole sequences (making backups) so as to be able to perform tricks of the trade on a copy.  How does it all work in real time?  We don't know that yet.  Lots more science is needed.

The problem with a lot of scientists, biologists etc. is they're victims of the die-out of "vitalism" versus "mechanism" in the great debates of the recent past.  The vitalists didn't have modern microbiology to draw from, to state their case.  The feedback mechanisms were hypothesized in a crude manner, the human imagination applying a rude sketch to nature's true face.  Now, a century and a half later, with more of that face revealed, the vitalist metaphors are more appealing, and what is language above metaphor, analogy?  Nature is alive, we know that, or do we wish Machine World as our only description.  It's more a decision about language than about Nature, as she is what she is.

My role at the church was outside security at first, a role I'm well used to playing.  In this case all that meant was directing ticket holders to one door, ticket buyers to another.  I had help.  I was wearing a thermal shirt under my coat and tie.  I had a large coffee from McDonald's (cardboard with plastic lid).  Certainly it was my privilege to welcome guests, not in any way an onerous duty.

Dr. Shapiro was right to pitch his talk where he did, as a science lecture that didn't try to dumb it down too much.  He knew he might have some real peers scattered in the audience, eager to suck down what they could.  His talk was high bandwidth in that the slides said a lot too, to those more versed in reading that kind of diagram.  Yet he was able to hold the attention of those just starting to get their feet wet.

It's not that we want to be superstitious about cells.  It's more that we want to not "misunderestimate them" (he cited George Bush for that one).  When challenged, bacteria respond like "knowing machines" that have had millions or billions or years to learn their tricks.  They're like transformers.  They don't just wait for mesons from heaven to throw the right switches in the face of adversity.  They're a lot smarter (more optimized for exaptation) than that.  As human beings with science, that gives a sense of where / how we might innovate, but also tells us more about what we're up against.

Dr. Shapiro said he'd given only two pieces of advice to the medical community:  wash your hands between each visit, and don't give them antibiotics unless it's really to save a life.  The latter advice is not just altruism.  Antibiotics wipe out a lot of friendly bacteria and if there's any surgery in this picture (say within six months), you'd have been way better off with your allies intact.  You kill part of yourself in other words (not unlike chemo then, in some ways).

The Q&A was all over the map, about cancer, about autism, about any given professional community's resistance to new ideas (memes -- microbiology in language).  Steve Holden and I slipped out just before the last question (he'd been ushering too) and headed over to the Heathman.  A very talented female vocalist was on the piano, with accompaniment, in the downstairs gathering.  We convened at the mezzanine level, per usual.  The wine and fish were excellent, as we've come to expect from this world class hotel.  I was grateful to have this privilege and gratified to see all this updating of world views happening.  Portlanders are staying in the loop at least.

My question during the Q&A after dinner was to cite the Pfizer guy's talk and ask if he felt walled out or otherwise denied access to what big pharma might be finding, behind closed doors.  The Pfizer guy was saying research was stagnating because playing it close to the vest, hoping to cash in big time with a few puzzle pieces, was not working out.  Researchers needed to put their cards on the table, for the good of everyone.  The liberal arts view.

Dr. Shapiro replied that he'd some time ago made the decision he couldn't afford that kind of profit-oriented seclusion for himself.  He felt the open source community (openly published science) was producing a flood of new findings, while being secretive was just shooting oneself in the foot.  As a geek, I could appreciate that analysis.

I used the "maxi taxi" for this one, finding less expensive parking than last lecture.  The crisp cold night air was welcome.  Mostly I'd been holed up indoors all day.