Thursday, 24 December 2015

Microcannons firing nanobullets

Sometimes I read papers that enhance my understanding of how the universe works, and sometimes I read papers about fundamental research leading to promising new technologies. Occasionally though, I read a paper that is just inherently cool. The paper by Fernando Soto, Aida Martin, and friends in ACS Nano, titled "Acoustic Microcannons: Toward Advanced Microballistics" is such a paper.

The grand scheme of this research is developing a tool that can selectively shoot drugs into cells at a microscopic level. This is hard because everything happens really slowly at the  microscopic scale in a liquid, in ways that meter-sized beings who live in air would not necessarily expect. For example, it is impossible for small organisms to move through a fluid using a repetitive motion that looks the same in reverse. For example, the way we move our feet back and forth to walk would not work for a tiny aquatic human, because the forward motion in the first phase of movement would be nullified by backwards motion in the second phase. This is why bacteria use things like rotating flagella to move*. Digressions aside, if you tried to shoot a tiny bullet through a cell wall, it would halt really quickly and diffuse away. Soto, Martin, and collaborators wanted to beat this.

They developed a "microcannon," starting with a thin layer of polycarbonate  plastic studded with small pores, which is a thing you can buy and don't have to make. They deposited graphene oxide onto the inside of pores in polycarbonate using electrochemistry, and then sputtering gold onto the inside of the graphene layer. The polycarbonate could be washed away with acid, leaving free-floating carbon and gold cannon barrels a few microns in size. While they were still in plastic membrane, the cannon pores were filled with a gel (literally gelatin from the supermarket) loaded with micron-sized plastic beads to act as bullets, and the "gunpowder."

The microcannons, loaded with nanobullets before and after firing.

Regular readers of my blog will remember that bubbles are somewhat of an exception to the small+water=slow rule, and that when they collapse it can lead to very fast motion on very small scales. So, the authors of the paper used perfluorocarbon (same structure as a hydrocarbon but with fluorine instead of hydrogen) droplets as a propellant, which they turned into bubbles with an ultrasound-induced phase transition. The bubbles collapse, leading to a pressure wave which drives the nanobullets out of the barrel towards their target**.

Composition and operation of the microcannons.
The authors wanted to characterize how powerful these things were, so they did two relevant tests. First, they embedded the cannons in an agar gel and loaded them with fluorescent beads. They looked at where the beads were before firing the ultrasound trigger at the cannon, and after. It was observed that they penetrated an average of 17 microns through the gel. I don't have much context to gauge whether this is a lot or a little.

The bullets were too fast to record with a microscope camera, so their second test involved recording the motion of the cannon after it fired the bullets. Naively one would expect to be able to calculate the bullet speed with conservation of momentum from knowing the cannon's speed, but momentum isn't conserved in a noisy viscous environment. They modeled the fluid dynamical forces acting on the system, measured that the terminal speed of the cannon was about 2 meters per second, and concluded that the initial speed of the bullets is 42 meters per second or 150 kilometers per hour. Pretty fast, especially for something so small in a draggy environment.

I don't know if this technology will succeed in the authors' goal of localized drug delivery to cells, but I think it's awesome that they made a functioning microscale cannon.
Oh the humanity.

*I recommend reading Life at Low Reynolds Number if this interests you.
**Or just in whatever direction it was pointing, I guess.

Wednesday, 2 December 2015

An old teacher hacking life itself: Christian Bok's Xenotext at MIT

This morning, I was googling for seminars at MIT that would provide lunch for me so I could avoid eating my own food which would bring me closer to havingö to buy groceries. I was planning on going to a fairly boring looking talk at Harvard about cell mechanics for a pizza dinner. However, I found a link saying that Canadian poet Christian Bök (pronounced "book") was reading from his new book of poetry.

I met Christian Bök in 1998 when he was my sixth grade teacher at a small school called Fieldstone. At the time I thought he was a great teacher; he always had lots of really interesting knowledge to share and would answer any question in an enlightening way. I thought he was the smartest person I had ever met. My friends often accuse me of knowing everything, but they are wrong. I don't know everything. Christian Bök knows everything. This was also the year that I stopped hating school and everything associated with it, and started becoming excited about learning new things. It is also around the time I stopped being one massive walking behavioural problem and started being someone that teachers would want to teach. I think Dr. Bök had a big part in both these things.

Some years after he taught me, he released his then-magnum opus, Eunoia, a book of poetry where each chapter uses only one vowel. So, the A chapter has passages like "Catamarans as fast as narwhals dash past sandbars and make ballast at landfall," while the U chapter has the coarser "Ubu untucks Ruth's muumuu; thus Ruth must untruss Ubu's truss." Each chapter is a self-contained coherent story. Eunoia put him on the map of the poetry world.

So naturally I was excited that he was at MIT today. So excited that I decided to forgo free pizza at Harvard and go to his poetry reading*. I also emailed his host mentioning that I was his old student and asked if there was time to meet with him. There was, so I met with him in the early afternoon. Fieldstone was a very small school and I was the most eager student so he has a decent memory of me. I imagine teachers are happy to find out that their students stayed in school, and boy did I ever stay in school. We talked for a bit about what I was working on, and its broad applications. I was quickly reminded of how sharp he was, as he quickly grasped the overview of my work and started asking tough and insightful questions. I mentioned that in 1998 I thought he was really smart. For the past fifteen years, through highschool, university, and grad school I have been surrounded by people who have been pre-selected for intelligence. I have met a lot of smart people. In this 20 minute conversation I got the impression that he was still the smartest person I had ever met. I mentioned that I had listened to the CD of Eunoia and that I liked the A chapter the best; he said he prefers I but most people like U.

After work I went to his poetry reading. His current project, Xenotext, is even grander and crazier than Eunoia. He plans to encode a poem in the genetic sequence of a bacterium, and when that gene is transcribed into a protein, that protein also reads as another poem in response. He wants to put this in the genome of an extremely robust extremophile, so that his poem will survive the death of humanity. I'll talk a bit more about this in a bit.

The poems in his book (not all of which will make it into the genome) generally have an apocalyptic theme, and draw a lot upon the Greek myth of Orpheus and Eurydice, about a poet who travels to the underworld to reclaim his lost wife. The first reading was a description of the destruction of the Earth through various man-made and natural cataclysms, which seemed to draw upon a lot of astronomical research (he mentioned Gliese 710 and Wolf-Rayet stars). It reminded me of the book Seveneves by Neal Stephenson, the best novel I've read this year**, which details aftermath of the moon's destruction and its effect on the Earth. He also read a short love poem, which sounded normal but he said took him five months to write due to the constraints he imposed on the writing.

After his readings there was a Q&A session and somebody asked him about the constraints on his love poem. He listed them off one by one, and they started normal and quickly got more and more extreme. First of all, it was a sonnet of seventeen lines and each line needed to have twelve syllables. Each line also had its own internal rhyming. The dedication of the poem was written as an acrostic in both the first and last letters of each line, so the first letter of each line read "FOR THE MAIDEN IN" and the last letter of each line read "HER DARK PALE MEADOW." To make the last letters line up, each line needed to have 33 letters (in addition to twelve syllables), so that they'd all fit on a grid. Then, finally, all the letters of the poem are actually a re-arrangement of all the letters in another poem by John Keats. I am no poetry expert but I thought that was pretty impressive.

Then somebody asked about the relevant biochemistry of his encoding the poem into a genome and getting it to read out another poem. He went on to explain it, and even when you don't include biochemistry it sounds insane. He made the analogy of encoding a text using a two-way cyper, switching let's say A with N, B with O, C with P, etc, but when you encode your sentence with this cypher, it makes another sentence. To do this, you have to choose an appropriate mapping between letters. If you start with A, you have 25 choices of what to make it, and after that you have 23 choices for which letter to map to B (unless you already mapped it to A) etc, so the total number of possible ciphers is 25x23x21... which is known as the double-factorial of 25, which is 7,905,853,580,625. So, find one of these eight trillion possible ciphers that will allow you to cipher English words into other English words, which I imagine is a very small subset, and Bök had the additional constraint of having to have it sound nice.

Ok so he eventually found a cipher that let him encode a poem into another poem, which seems like a huge accomplishment to me, but then he had to encode this into the genome of a bacteria! The way genes work is that there is a DNA sequence written in the four letters of A, T, G, and C, and the DNA is copied into a complementary RNA strand. The RNA goes through this little cellular machine called a ribosome, that concatenates amino acids onto a protein chain. There are twenty-three amino acids and only four nucleobases, so  combination of three bases is required to tell the ribosome to add a given amino acid to the chain, which it does by following the genetic code (which is not the same as your genetic sequence). For example, if the DNA reads CAG then the amino acid glutamine gets added. Each gene codes for one protein (there is a combination that essentially acts as a period and stops the transcription), and one protein does one chemistry thing. He didn't go into the details, but in order for his project to make sense, he would need a mapping of three bases to one Latin letter (unless he restricts himself to a 16 letter alphabet), and then another mapping of amino acids back to Latin, either using a 23 letter alphabet or using pairs of adjacent acids to make 26 letters. He would have to choose his mappings between Latin, DNA, and proteins to work as a poem. THEN he would have to engineer this gene and implant it in the genome of a bacteria, not have it die, and have it actually produce this protein. This could be verified through genetic sequencing on one end, and protein sequencing on the other.

The central dogma of biology and poetry. Source.

It turns out he actually did succeed at doing this, implanting a poetic gene into E. coli which produces a poetic protein. They are called Orpheus and Eurydice respectively. The first poem, which he read at the reading, begins "any style of life / is prim..." and the second begins "the faery is rosy / of glow..." Apparently the Eurydice protein is also fluorescent (he used a supercomputer to see how each proemtein would fold),  so you can tell when it's expressed. His next step is to implant this in the extremophile.

I have a deep respect for ideas that seem too crazy to work but are attempted anyway. This is the craziest such idea that I have heard of. After the reading I bought his new book, which he signed. It also has a lot of biochemistry-themed poetry in its explanation of the project, for instance a poetic ode to each nucleobase and poems where the words end and start with complementary base letters. I look forward to reading it.

It was a nice surprise re-acquainting myself with Dr. Bök  today. He is a truly impressive human being, and had a big effect on who I am today.

*It's ok though because I found free pizza anyway.

**The worst is The Land of Painted Caves by Jean M. Auel. Do not read this book.