Tracking Bioengineered Bacteria Through The Body Using Ultrasound

Each of our hundreds of trillions of cells is as complex as a big city, and the mere shape of our internal organs reveals little about the true complexity of life. Unfortunately, you can’t “see” biochemistry, at least not with the naked eye. However, advances in molecular biology are literally illuminating the chemistry going on inside living tissues.

Scientists at the Shapiro Lab at Caltech have engineered bacterial cells that are exceptionally visible to ultrasound imaging. This technology could finally allow scientists to “watch” the biochemistry going on deep within living animals.

Since the 1990’s, there has been a fluorescent protein revolution in molecular biology. These fluorescent proteins are engineered to emit light from cells that express whatever gene scientists want to study. Unfortunately, unless your animal is translucent, they are not much use in illuminating the chemistry of internal organs. If you want to know what’s going on deep inside, you are limited to the static and specious snapshot of a dead and dissected animal.


Mouse engineered to express Green Fluorescent Protein (GFP)

Ultrasound imaging, on the other hand, is a great non-invasive technique to see inside a living body. This is the same technology that has us staring at amorphous black and white images trying to figure out how cute our future child will be. Ultrasound imaging uses echolocation, emitting sound waves (at a much higher pitch than we can hear) and recording their reflections from different internal tissues, turning them into a 3D image. Until now, ultrasound imaging only revealed internal structure, not the chemistry, gene expression, or types of cells in those deep tissues. However, the Shapiro Lab has engineered bacterial cells that specifically ‘light up’ under ultrasound.


Embryo at 14 weeks

How? Tiny balloons. Some bacteria in nature already make tiny gas-filled structures inside their cells to help regulate their buoyancy. Because of their size, these balloons happen to vibrate at the same frequency as the ultrasound wave, strongly reflecting the ultrasound signal. Obviously, these natural structures did not evolve with ultrasound technology in mind, so they had to be further engineered or tuned like tuning a guitar string or drum head. The Shapiro Lab did this by combining pieces of genes from different bacterial species to get the best ultrasound signal. Despite occupying roughly 10% of the cell’s volume and 1% of the cell’s mass, the balloons only marginally impaired the growth and movement of the bacteria.

An additional feature of these balloons is that they collapse when subjected to a suddenly strong pulse of ultrasound, like a glass shattered by an opera singer’s voice. The authors demonstrate that the balloons can be engineered to collapse at different pressures and frequencies, enabling different populations of cells to be distinguished within the same tissues, adding color to the gray ultrasound image.

As a proof of concept that these bacteria can be observed in live animals, the Shapiro Lab injected a chunk of gel that contained the engineered bacteria into the colon of a mouse. They used a species of bacteria that occurs naturally in the gut and is often used in humans to treat digestive disorders. Indeed, shape and location of the bacterial gel inside the mouse could be imaged with high resolution.

They were also able to image cancer tumors using this technology. Special strains of bacteria have already been engineered to bind to cancer tumors and even inhibit their growth. By giving these cancer-tracking bacteria the balloon-making genes, they successfully imaged a mouse tumor using ultrasound.

Bacteria can be easily engineered to stick to a variety of specific tissues, and have the potential to serve as ultrasound homing beacons for imaging various tissues in both research and medical therapy. Other applications include tracking the spread of newly introduced bacteria into our gut and the dynamics of our bacterial ecosystem. Many medical disorders are caused by imbalances in our gut bacteria and require the introduction of new bacteria into our body to correct the imbalance. Better understanding how and where these bacteria spread within us will better direct future treatments and innovations.

One of the Shapiro Lab’s most ambitious goals moving forward is engineering animal cells to manufacture these ultrasound balloons. However, can animal cells make this bacterial structure? Would the presence of these balloons affect the way animal cells behave? Would they stimulate an immune response? Can they be used in a therapeutic context? If these hurdles can be cleared, the impact of ultrasound markers like these could be an extraordinary new tool for research and medicine.

Politics, Uncategorized

Country Over Party?

It was perfectly reasonable, though disappointing, for pro-life, pro-corporate, anti-tax Republicans to support Trump as their nominee, despite recognizing all of the obvious and disturbing aspects of his character. There was no shortage of rational, non-bigoted Republicans who knowingly voted for a racist, stupid, misogynist who was wildly unfit and unprepared to become the most powerful person in the world, voting merely so that they could get the judges and tax rates that they wanted. It is the inevitable byproduct of the two-party system, choosing between the lesser of two evils. The American left would have probably done the same had the shoe been on the other foot.

Now, Donald Trump is president, and the West Wing is crawling with reactionary Republicans. Neil Gorsuch will reign supreme, and Paul Ryan will have at least two years to pass sweeping, conservative legislation. Nothing will change without action from Congressional Republicans. However, even the most reasonable, responsible congressional Republicans still refuse to push back against Donald Trump with respect to Russia, corruption, and civil rights. The left is correct to accuse GOP leaders of putting party before country. That is a refrain worth amplifying.

However, before the left turns the smug disdain up to 11, let’s test this accusation of ‘party before country’ for validity and hypocrisy…

If, for the sake of argument, all Republicans care about is abortion and tax policy, it’s in their best interest to stand by President Trump. They need the Republican White House to be politically strong for the sake of passing legislation and re-electing a Republican president. That’s what we mean by putting party before country. Single-issue voting may be effective, but it produces an immoral disregard for the complexity of federal policy and the number of issues that are critical to consider when stepping into the ballot box. Don’t be a single issue voter. Don’t do it.

Let’s consider hypocrisy. Would Democrats be willing to put country before party? Fortunately, we weren’t forced to vote for a Trump-of-the-left, but liberals will have the opportunity to show their true colors very soon. If Donald Trump truly represents an existential threat to the country, and if Donald Trump must be defeated for re-election at all costs, who should the Democratic Party nominate for president in 2020?

The Democrats may be able to defeat Donald Trump with a liberal like Bernie Sanders or Elizabeth Warren. They may be able to elect an establishment pick like Tim Kaine or Corey Booker. However, there is risk in that kind of choice. Such a general election will be another polarized slug fest, pitting left v. right over a few million votes, an election that could turn on a dime and risks a full four more years of Donald Trump with his finger on the armageddon button.

The Democratic Party can make a patriotic choice to ensure victory in 2020, but it requires putting their money where there mouth on Donald Trump and putting country before party.

They could nominate a moderate Republican. It’s not a comfortable thought, but it would transcend the ideological divide to produce an election about character, fitness for office, and experience. After all, the presidency isn’t supposed to be ideological.


Jon Huntsman, the only guy to look more presidential than Mitt

Jon Huntsman, who has advocated for a third-party since his presidential run in 2012 would be an ideal choice for me in this scenario. John Kasich, who was supposedly every Democrat’s favorite Republican in the 2016 primary, has to be on this list. However, his views about religion make him a nonstarter for me. Bill Weld is a highly qualified, former VP nominee of the 2016 Libertarian ticket and flirted with endorsing Hillary Clinton in 2016. Democrats could have a look at famous swing votes Susan Collins and Lisa Murkowski from the Senate. Jim (RamboWebb is practically a Republican who probably voted for TrumpBob Dold is a youngish, socially liberalish, pro-choiceish Republican Congressman from Illinois who has been trading his job with Democrat Brad Schneider every 2 years. Colin Powell is too old, but perhaps a non-partisan administration official can come forward.

Would this work? Probably not. It would almost certainly elicit a third party left-wing revolt. However, consider that every problem with this scenario also applies to Republicans choosing to defy President Trump. How does the left’s characterization of Trump have any credibility while nominating someone from the left who forces rational, non-bigoted Republicans into the same choice they had to make in 2016?

Before you accuse Republicans of putting party before country, question if you would do the same. Put yourself in their shoes.


Paul Ryan is Actually Right About Planned Parenthood

I’d hate to say it, but Paul Ryan was right about Planned Parenthood in his recent CNN town hall. Funding PP does ‘effectively’ fund abortions with taxpayer money. All the meticulous accounting that PP is committed to can’t prevent non-abortion revenue (mostly from medicaid) from paying for staff, PR, utilities, and infrastructure. However, Ryan has a tough road ahead of him to clean up the confusion.
Speaking of roads, the federal government funds the transportation that gets people to abortion clinics. Taxpayers fund the abstinence only education which has demonstrably lead to more abortions. Taxpayers fund elections that occasionally elect people who fight to keep abortion legal and accessible. The federal government even pays millions of federal employees, some of which occasionally purchase abortion services! Clearly Ryan has a lot to clear out of the federal budget.
Check Your Outrage

Safe Space Trigger at U of C

It’s been a while since I’ve posted. I’m in the throws of writing my paper/thesis, though I don’t know if that makes me inherently less likely to post out of time constraints or more likely due to procrastination.

The University of Chicago, where I work/study/serve-“the man”, published the following letter to its incoming Freshman class:


The letter has drawn national attention, smug satisfaction from many of its alumni, and trepidation from the incoming students. There’s undoubtably a generational divide here, one that I find myself in the middle of. Adam Davidson put it well in the latest Slate Political Gabfest:

“I don’t know if college-age kids understand that people in their mid-40’s think of themselves as like, ‘oh, I just graduated from college’, but that is my continual experience, to remember that, ‘oh, I’ve been alive longer after college than before college’. And, so this whole world of trigger warnings and not allowing people on campus to disagree with you… […] This is when I feel like an old man and very confused and upset, and I was just proud of my alma mater, the University of Chicago, which sent a letter to the incoming class of 2020 saying ‘we’re not into that; we don’t do trigger warnings; we don’t shield you from complicated ideas. This is a place where we wrestle with complicated ideas, upsetting ideas, the world as it is.’, and I felt very proud of the University of Chicago. I also felt like, maybe this letter was written by a bunch of people just like me and were completely missing something really important we don’t understand.”

Perhaps as a 29-year-old, I can walk that generational divide. This letter and Adam’s response reminded me of this old Simpson’s clip:

Adam and the University of Chicago have taken a righteous stand, but nuance is important in preventing an adversarial or authoritarian environment and backlash from the students…

Take trigger warnings: If you are teaching a class, leading a discussion, or showing a video of an event that is likely to be a psychological trigger to traumatized students, it is compassionate to warn students of this beforehand. This is especially true in the case of sexual assault, since college students live under such threat and are far more likely to have been recently been survivors of rape.


On the other hand, no one should be forced to give trigger warnings or even be censured for eschewing them. They can detract from many presentations and discussions, so should be used sparingly.


Safe spaces provide a necessary escape from stressful environments. Whether it’s your dorm room or an exclusive club, they have value. I started a chapter of the Secular Student Alliance primarily to serve as a safe space for atheists to express themselves and form a community. The ability to temporarily retreat from the chaos and rigmarole is critical to student development.


College itself is not inherently a safe space. On the contrary, it’s supposed to be ideologically challenging. Whatever ideological safety you impose infringes on the expression of others.


The University of Chicago’s letter does not, as some have reported, limit or discourage protest. Protest is a form of expression that the letter specifically endorses.


It should be news to no one that protest often takes the form of silencing others. Shouting down invited speakers, blocking entrances, and destroying property are anti-expression


The best solution for bad speech is more speech, and neither I, nor this letter (for the most part…), says otherwise.

[Edit 8/30/2016]: A friend of a friend from U of C did a nice survey of reactions to the letter.


This Stupid Poem I Wrote

“Life Isn’t Fair” by Ben Zalisko

“I don’t understand”, said the boy to his mom
Why I’m not allowed to go skating with Tom
“Life isn’t fair”, she said squatting in place
and thumbed away dirt from his obstinate face

Far away, dad left work for the very last time
After decades of outstanding work on the line
“It’s out of my hands, Jim, the math is the math
I can’t pay your wages when others take half.”

The manager, Steve, got a call from his boss,
“It is what it is, Steve, a loss is a loss”
The owner’s son, barely a month out of Penn
said, “I’ll want to be fair, Steve, my door’s always open.”

The businessman said to his staff, “It’s not fair,
But we can’t allow this sort of unruly flair
As professionals, we all must dress to impress
We can’t cause our customers any distress.”

The assistant left work to find her car in the lot
With a ticket for parking in an unauthorized spot
“The law is the law”, said the meter maid in her coat.
Sam took the ticket and drove off to go vote.

She looked at the names, at the lessers of evils
Of candidates chosen by very few peoples
That is the system we’ve always endorsed
A poverty numbed by the thought of what’s worse

José couldn’t vote because in the land of the free
Your birthplace means more than your allegiance since three
Without an ID, the same fate for his wife,
And Frank’s short jail term debars him for life.

The law is the law, and life isn’t fair
We can’t create money from the thickest of air
We have little control on the choices of others
Least of all mothers and much older brothers

With fairness presumed, questions abound
We all want to understand why our world isn’t sound
What frustrates me most, from birth to the grave,
Is that so many people consider tautologies satisfying

…as if a simple statement of what is, “is”, somehow justifies a shirking of responsibility, absolves us of guilt, or is even an explanation at all. “Life isn’t fair”, “That’s the way it is”, or “those are the rules” should give no one comfort, but serve as prompts to make change. Basking in our inability to articulate a problem or an explanation leaves us prey to the few, giving them license to make our lives for us, Gus.


Food for thought during party primaries and conventions…


I’ll Give You Four Years of Trump for Self-Driving Cars

Let’s get our priorities straight. 37,000 are killed and 2.35 million are injured on the road every year in the United States. That’s more than double the rate of US deaths in the Vietnam War at its absolute peak. That’s more than 8 times as many US deaths in 1 year as the entire Iraq war. Worldwide, twice as many people die in car accidents than in all wars and murders combined. Fuck the peace movement, give us self-driving cars. Ok, don’t fuck the peace movement, but let’s prioritize.

Car accidents cost the US $871 billion per year in “economic loss and societal harm”. That’s twice our federal budget deficit. Two years of dramatically fewer accidents would pay for the entire Iraq war. It wouldn’t pay for Trump’s $1.2trillion/year taxcut, but it gets most of the way there.

Think about the thousands of dollars each of us would save in car insurance. Imagine the revolution in public transportation with self-driving busses. Imagine the changes in traffic patterns when networked, self-driving cars can reach higher highway speeds traveling inches apart. Imagine ending… ENDING stoplights and stop signs. Networked cars won’t have to stop for each other. Imagine what that does to mileage and our carbon footprint. Imagine how food and goods will be cheaper because the highways remain the best way to move shit around. Imagine not having to find parking when everywhere in america has a free valet. Imagine no more DD’s!

Imagine the economic impact of having more time in the day and more job flexibility with better commutes. The talk about robots taking jobs tends to ignore the increases in productivity and economic growth that result, the rising tide that raises all boats. This is a perfect example of the benefit of safety, money, jobs, and general wellbeing that vastly outweighs the truckers and bus drivers who have to find new jobs in that new economy.

This isn’t cold-fusion; the technology is here. (Although, don’t get me started on the feasibility and impact of a fusion energy revolution) Self-driving cars will probably be a significant part of highway traffic in the next decade.

However, as with any new technology such as attack drones, lab grown food, and gays, there’s an “ick” factor reaction to the unknown. One of the biggest limiting factors is lawmakers, as self-driving cars are mostly restricted to use on private property. Tesla is anticipating the revolution, making its cars capable of driving themselves, so they will be ready when the law and infrastructure catches up.

So far, self-driving cars have an impeccable record. By far the biggest danger that driving robots have to deal with is humans. Even the first crash in which the car was partially at fault, which didn’t happen until 2015, was mostly the fault of an aggressive bus driver. When self-driving cars become part of our infrastructure, the path to criminalizing manual driving will begin in earnest, as it should. There will aways be places in our country where people can drive for fun, but in a culture where the drivers we share the road with are already all “idiots” and “assholes”, I don’t think kicking them off of our highways will be too difficult.

Who is willing to rely on Congress and state legislatures to push the progressive changes we need in infrastructure to make this happen? Who is willing to count on trillion dollar investments that will lead to a huge… YUGE return on investment? How many lives will be lost while we wait?

I’m certainly not the early adopter type. I only got my first smartphone a few months ago. Really. I also know that sharing the road with 4,000 pound robots moving at 70mph would freak me out, let alone riding in one. I don’t even like roller coasters. I also think putting newly developed drugs into my body would be unnerving, especially if I’m not that sick. However, if I’m dying of cancer, I’ll accept more risk for the newest, most badass technology.

Revolutionary drugs that are found to be effective in early trials can be given “breakthrough status”, and used for many terminally ill patients before the drugs have passed all their safety trials. We are willing to accept some risk of the unknown for a chance of fixing a dire known. People will surely die in accidents caused by self-driving cars, but let’s keep our perspective.

Driving is such a necessity that we are well conditioned to ignore the costs and risks. Many Americans don’t know how sick we are, hurling our bodies into one another and our glass and steel cages. Many Americans don’t realize how close we are to a cure. We can’t afford not to be early-adopters when it comes to self-driving cars. Every candidate needs to speak on this issue, and every presidential candidate should put forth a plan.

Truly revolutionary ideas put our political fears into perspective, but fortunately, Trump for self-driving cars isn’t a choice I have to make.