The Physics of…

A blog…that will occasionally discuss biophysics.

12/5/18 – LB

This one is for the true microbiologists, but just for context for anyone else, "LB" is the most common growth medium used for bacterial culture, and is used in nearly all molecular biology labs...

My buddy Eric invited me to give a talk at the University of Florida last week; UF is in Gainesville, which is a surreal place, as far from a beach as you can get in Florida, in the middle of the dense nearly tropical forest. There are wild alligators and snakes on campus, and Spanish moss drapes the trees. The day after my talk we went to another talk at the Veterinary school about the evolution of pathogenic bacteria in your gut during infection; one of the questions at the end was by an old professor who would make a good Santa Claus, except maybe a little too short, but with long white hair and beard.

Eric: "Do you know who that is?"


"That's Roy Curtiss. He's apparently pretty famous, a member of the National Academy (of Sciences)."


Through a twist of fate that I won't go into, that night I ended up at dinner with Roy and a few other professors, including Roy's wife Josie. Roy sat next to me and was mostly quiet as he focused down on his soup and pasta, while Josie, who is an adorably bubbly little midwesterner, sat up straight across the table from him and smiled. Roy wore a blazer with a chicken pin - it turns out much of his research had to do with chickens, like, how to keep your chickens from getting infections I guess. He had a something of a journeyman career, originally from New York, studied at Cornell, and then moving from Washington University as a professor, to University of Alabama at Birmingham, where he built the premier medical center in the south, and then on to the University of Arizona and Florida. He was from the second great wave of molecular microbiologists (succeeding the original Phage Group, all of whom he knew), who built many of the molecular tools that we still use today in molecular biology, and after he ate and had a couple glasses of wine he told stories about the glory days, which indeed, were incredible times in biology.

Near the end of the dinner the table was indulging in conversation about strain collections - a microbiologist may collect tens of thousands of bacterial strains, that they either isolated or constructed, during the course of his or her career. Most of them are going to be strains of E. coli, which is the workhorse of molecular microbiology and is where most genetic engineering is done. E. coli grows in LB media.

Roy: "By the way, do you know what LB stands for?".

Most scientists think LB stands for "Luria Broth" or Luria-Bertani Broth," because Giuseppe Bertani created the formulation when he was in Salvador Luria's Lab at the University of Indiana (Luria won the Nobel Prize for reserach into bacteriophage (i.e. a bacteria virus) replication). But if you know better, you know that Luria was trying to steal credit from Bertani by appending his name to it, and that Bertani himself meant LB to stand for "Lysogeny Broth" because he was studying lysogeny (where a virus integrates its DNA into the bacterial chromosome) when he formulated it. So we all smugly laughed around the table and said "Yeah! Lysogeny Broth, but most people think its blah blah blah..." But Roy huffed:

"Bullshit!...Liz Bertani...LB"

Apparently Liz Bertani, Giuseppe's wife, was a technician in Luria's lab, and she, not Giuseppe, had formulated LB, and used her initials to name it (as we do with many things in microbiology). In the end, Luria had stolen the credit from Giuseppe, who had stolen it from Liz. LB.

11/25/18 – The Physics of Prison

Academics talk about the depth of prison, the feeling of being submerged below the surface upon which society floats.

The W train (mustard yellow line) goes straight from Washington Square to Queens Plaza, an emblematic Gotham-style subway and el-train center in Long Island City (Queens). After you get out, you have to go over on Jackson Avenue, under the 7 train (purple line, the minor light purple on morning glories), across a vast and desolate half-finished gravel train yard with cement pylons, rebar, trains tracks, and puddles, down past a cheap furniture show room (everything 70% off), and then angle down onto Van Damn Street. I’m usually late so I run. Queensboro Correctional Facility is a nondescript cubic building, albeit with metal gratings over the windows, on Van Damn, across the 47th Avenue from La Guardia Community College. Once you go in, you enter a different reality, no matter who you are. Time and movement slow, your brain activity slows. The guards who are there everyday are constantly forgetting what they’re doing. You sign the log book and slide your driver’s license through the office window to them, and then they buzz you into the locker room behind you where you put your bag and all the stuff in your pockets, then they buzz you back out once they see you’re ready. Then there’s some unnecessarily long lag time before they call someone to take you up to the classroom, and usually they forget you’re there, even though you’re standing right in front of them, so it’s even longer. Everyone inside (you, the guards, the guys (I can’t bear to write the pr*s*n*rs or the inm*t*s)), once inside, is trying to suppress something dark - it’s the darkness that is latent in most of us, that Kafka expressed, founded on confusion and pain. If you can suppress it until you get out, you’ll likely be okay, but it’s a matter of time and discipline. Suppression of this dark thing causes confusion, memory loss, it scrambles the brain, like oxygen deprivation. You’re inside prison, ironically, suppressing this dark thing: within prison itself is the dark thing that society is suppressing. Prison in America is the collective suppression of the memory of slavery. Had there not been slavery, society wouldn’t feel as strongly about not only locking up black men, but submerging them, cutting them off from daylight, food, women, and then trying to forget them, suppressing them within the public consciousness. But they are there, and the dark memory is latent within us.

A guard slowly walks you to the elevator (unto the 3rd floor, though all is submerged). Many of the guards at Queensboro, maybe half or more, are black women. Queensboro is also a re-entry facility for guys who have only 6 months or so left on their sentence. I wonder if they do that on purpose, put a lot of women around the guys to reacclimatize them to what it is like to be around women. Perhaps not. At the upstate prisons, like Sing Sing, most of the guards are white, because it’s white people who live in upstate New York. This creates a dichotomy between the guards and the guys, and dichotomies, as history has shown us, sow hatred. The mood is more relaxed, albeit subdued, at Queensboro. It’s but a matter of time before the guys get out, and there’s little reason except for fear for either the guards or the guys to start something. The guys wear dull forrest green prison uniforms. We wear bright kermit green T-shirts. The classroom where we tutor has the feel of a school as I imagine one to be in 1984 (Orwell. On the train to my shift I saw a guy on the R train wearing a hat that read “Make Orwell Fiction Again”) - dull whitish-yellowish painted cement walls, classroom norms on butcher paper taped up around the room, a TV complete with VCR, and a whiteboard on wheels but no dry erase markers. And of course, gratings over the windows - all you can see when you look up and out is a billboard for a cellphone company.

Mason is 29 years old, and’s been in prison since he was 18 (it makes me shudder to write). He’s tall, built like a professional football player, with huge forearms; he has smooth, shiny, dark skin, big lips, half closed dark eyes, and sharp cheek bones that give way to concave temples. His hair is very short but wavy, especially in the front of his head. The underlying principle behind Mason’s attitude and response to almost every question that we discuss has to do with freedom. The same goes for most of the guys with whom we’ve had any in depth conversation. For example, Mason’s taking a public health class. On the subject of smoking and sugary drinks, him and his classmates are staunchly against any sort of regulation because they should be free to do whatever they want to do. The are also staunchly against taxes of any kind. In this sense, ironically, they have Republican, even Libertarian politics. And when I think about it, this shouldn’t be a surprise: all the system has ever done for them, especially the young guys, is put them in jail. Their tax dollars, when and if they pay them, are not coming back to them in any positive sense, only a negative sense, insofar as they fund the prisons. “All the politicians are doing is lining their pockets, y’see what I’m saying?“. On the other hand, on the subject of other public health crises: the opioid crisis, Flint, Katrina and, more broadly, the racial and socioeconomic disparity in public health, the guys all agree that the federal government, while it may have failed, should be the agency to respond, and therefore on these matters have liberal politics.

Mason’s also taking sociology class from La Guardia Community College. Discuss the connection between truth and freedom (kind of a ridiculous assignment when you think about it). What is the difference between objective and subjective truth (a really interesting assignment when you think about it; neither have anything to do with sociology as far as I can tell). “Isn’t objective truth like when you kind of sugar coat the truth but subjective is when you just say it flat out?” The difference between objective and subjective truth is a very deep question and almost certainly a false distinction on a philosophical level. It’s also a prescient question in the post-truth era. I assumed I knew what the assignment was after. “The world is round is an objective truth, because it is universally accepted as true and there is evidence to support it. Jesus Christ was the son of god is a subjective truth because it is not universally accepted as true, but for those who strongly believe it to be true, it is their subjective truth. So now, before we knew the world was round, everyone thought it was flat, and there was evidence to believe it was flat (it looked very flat). So before we realized the world was round, was the statement ‘the earth is flat’ an objective or subjective truth?” “I would say it was an objective truth because everyone believed it.” “I would agree with that, which is weird because it means you can have something that’s objectively true, even scientifically true, at one time that actually becomes false at another time. Let me give you another example: Trump said more people who came to his inauguration than Obama’s even though in the photos it’s clear that way more people were at Obamas, and then many Trump supporters believed him. So is the statement ‘More people came to Trump’s inauguration than Obama’s’ an objective or an subjective truth?” “Well I would have to say...neither.” “Haha, exactly, its simply false. Which is weird because, if that’s correct, then the belief in something is not necessarily enough to make something even subjectively true.” I got up and closed the door so the guard couldn’t eavesdrop. “Let me give you one more example of objective versus subjective truth.” This was going to be the punchline, and I assume what the assignment was getting after. “You and I both live in America, but we have different experiences. You have your subjective truth and I have mine. For example, you have your subjective truth as a black man and I have mine as a white man. So describe your subjective truth and how it might be different from mine, even though they’re both true.” Mason became animated and loud. “O man…” We talked about what you might expect. The police, as they often do, came up very fast (Mason’s best friend in high school was white, but wasn’t the target of as much police attention as Mason). The hood, the streets, friends, prison…truth, as such, was quickly forgotten as a topic of conversation and we simply talked about his past and his youth in East New York.

Only a few guys come to the study hall each week even though others are enrolled in the classes, but the study hall selects for the guys who see it as an escape from the cell blocks, which are aggressive, loud, and tough. It also selects, I think, for the guys, like Mason, who are hopeful and even optimistic about their future life on the outside. “I have to take advantage of this oppor-tunity. I’m not coming back here.” This optimism is both inspirational, in light of their circumstance, and terrifying, in light of their prospects. Mason wants to go to school for music production. He also, adorably, is in love with my fellow volunteer Nina, who is.a beautiful and gentle 23 year old black girl from Milwaukee, who’s interviewing for medical schools. “Yo I gotta tell you I am crushing on Nina,” Mason said with a wide smile as he leaned over his desk (Nina was away on an interview that week). Me and Gordon (the third volunteer, a good wiry middle-aged Brooklyn guy) looked at each other under our brow and laughed. “Well, y’better stay in school, if you want a girl like that.” “I know, but sometimes that’s what it takes, is that moti-vation.” In prison, you’re submerged. Submerged below the surface of society, submerged within your mind. I worry it’s actually too easy to be optimistic before you get out because you are not yet confronted with the brutal reality of the ex-con, and once you are, without any support, you’re fucked. We all suffer from more mundane, mini versions of this psychology: whereby we promise ourselves to change, but fall back into habit for lack of external incentive or support. There is no free will, and there's no personal responsibility - we're all subject to the state of our minds and the state of our circumstance, including our history. We need to pretend as if there is personal responsibility, on some level, to keep the order I guess, but there's really not at the heart of things. It's critical to keep this in mind - there's no way you would lock a teenager away for ten years and forget about him if you believed it to be so. But hope and optimism aside, Mason is sharp, he’s articulate and writes well, and he’s good, with a broad smile. He can succeed I and think he might, even if there is no connection between truth and freedom for him, certainly not between his subjective truth and his freedom.