Monday, May 01, 2017

Explaining CAR T-cell therapy with marshmallows

Last week, I had fun giving a guest lecture at my daughter's preschool on some cutting edge synthetic biology research. Part of what made it so fun was figuring out how to communicate the essence of the subject on an appropriately comprehensible level.

My daughter's class has been learning about the body, things like muscles and bones and the heart and blood.  One day a few weeks ago, she came home bubbling with excitement about having made blood out of candy that day: into some diluted corn syrup (plasma), they put mini-marshmallows to be white blood cells, red cinnamon candies to be red blood cells, and sprinkles to be platelets. I thought this sounded awesome, and it inspired me to build on that for a lesson about CAR T-cell therapy.

For this lesson, you will need white, red, green, and orange mini-marshmallows, food coloring, and toothpicks. The white marshmallows are white blood cells, the pink ones are healthy cells, the green ones are germs, and the orange ones are cancer cells.

Dip the toothpicks into the food coloring, then poke them into marshmallows to make patterns of three colored dots on the marshmallows. Put patterns on the marshmallows as follows:

  • Give all of the pink healthy cells the same pattern.
  • Give the orange cancer cells a pattern that's almost the same as the healthy cells---but with one difference.
  • Give the germs patterns that are quite different from the pink healthy cells.
  • Give the white blood cells patterns that match germs, but not the healthy cells or cancer cells.

Remember that marshmallows can get flipped around, so "red-red-blue" is effectively the same as "blue-red-red"!

You should now have a bunch of marshmallows with patterns on them.  The lesson goes like this:

  • All cells have patterns of chemicals on their outsides (Show some patterns).
  • White blood cells tell which cells are diseases by matching patterns (Show some white blood cell patterns).
  • A white blood cell leaves your healthy cells alone because they don't match (Show a white blood cell not matching a healthy cell)
  • The white blood cells learn the patterns of diseases and when they match the germs (Show a white blood cell matching a germ), they kill the germ (Eat the germ marshmallow).
  • But cancer cells are tricky, and sometimes their patterns are too close to healthy cells for the white blood cells to learn their patterns (Show how the cancer cell and healthy cell patterns are similar).
  • But now there is a new type of medicine people are trying to make work, where we can take some white blood cells out and teach them a new pattern to recognize (Take a white blood cell and mark it with the cancer pattern).
  • Now we put the white blood cells back in, and they recognize the cancer (Show how the pattern matches now) and kill it! (Eat the cancer marshmallow).
That's CAR T-cell therapy in a nutshell in 5-7 minutes, minus all the details and the cautions and concerns. I had great time teaching this class, and these 3-5 year old kids asked really good questions, like "Does everybody have white blood cells?" and "How do you teach the cells the patterns?" so I think they learned.  

And as I was writing this, my daughter arrived home, bringing a heartmeltingly lovely thank you card her classmates had made.

I think that her class got it.  Science communication win!

Monday, April 24, 2017

The edge of science is never far away

My preschooler daughter started her bedtime routine rather late tonight, because I am always a sucker for certain types of questions. Tonight, she asked about how our lungs move air in and out. That led to how the heart works, then how muscles work, which zoomed in and in through fiber bundles to individual cells, fibers within the cells, and actin and myosin.

Each picture or diagram came with a "And what is inside that part? [point]" until we were looking at an actin protein, then a molecule of ATP, an oxygen atom, and finally the stark and simple table of the standard model itself. What's inside an electron? Nobody knows, or even if that question really makes sense. We know somebody who's working with CERN on the Higgs. Quarks have really funny names.  We're out at the edge of science and I'm grinning and telling her that when she grows up, she could be a scientist and help try to find out the answers to all of these questions.

We know so much about our world, remarkably much, but the nearness of the edge of science continues to exhilarate me. It doesn't take many questions to get you out there, and the path is simpler than many realize. Our children can walk it easily, if we do not discourage them and if we smile and appreciate the "I don't knows."

After Harriet gets out of her bath, we're going to omit the usual bedtime story and watch "Powers of Ten" instead. I'm looking forward to it.

What it takes to do an interlaboratory study

In another step of my ongoing quest to make synthetic biology engineering simpler and reliable, my collaborators and I are starting another big interlaboratory study focusing on precise measurement of fluorescence. We're now in the very nervous part, where all of the samples of material that everybody helping out with the study is going to measure have just been shipped out, and I'm hoping that the numbers that come back will be nice and tight, just like the preliminary study showed. 

It takes a lot of work to put a study like this together---much more than I would have anticipated before I started doing this sort of thing. We've spent several months figuring out how exactly we want to run the experiment, and documenting it all as precisely as possible in order to make sure everybody does it the same way. Then my colleague Nicholas at MIT spent quite a bit of time over the past 24 hours preparing 875 sample tubes and packing them into boxes. As Nicholas put it: "On a completely unrelated note my lab is currently low on Eppie tubes."

Nicholas DeLateur preparing samples for shipment.

One step at a time, of such careful and unglamorous work, does science and engineering move forward, and I am grateful for all of the people I have found who understand its value and join in working together on such steps.

Thursday, April 20, 2017

Reducing DNA context dependence in bacterial promoters

Swati Carr's work on insulating promoters is now out as an article in PLOS ONE, with me and Doug Densmore. I've talked about this work before, and I'm very happy to have been involved in it as something that I consider a very solid piece of engineering.

Basically, promoters are the "control switches" that determine how much a gene is expressed, and which other chemicals in the cell can regulate that expression. The problem is, at least in bacteria, that the promoters we usually use are extremely sensitive to what you put in front of them---even to the point that the tiny "scars" left in the DNA sequence from stitching genes together can have a radical effect on their operation. With Swati's method, Degenerate Insulation Screening (DIS), we now have a simple "shake and bake" engineering method for insulating these promoters, which works very well to make a promoter behave consistently, despite changes in what is placed in front of it.

Let me illustrate it very simply, with two images that I suspect will be clear to even a non-synthetic-biologist. In these pictures, the green and red bars show the behavior of two genes in a bunch of different variations of a small circuit. The more similar the bars are, the better, because it means the genes are behaving more reliably.

In short, this is your circuit:

This is your circuit without DIS:

Any questions?

Thursday, April 06, 2017

Grace on Biology

I just made this image for a talk introducing ideas in synthetic biology to programmers, and cannot resist sharing. Bonus points if you recognize one of my scientific heroes without help. Images courtesy of Wikipedia.

Thursday, March 09, 2017

Predatory publishers "cloaking" themselves with Editorial Manager

It appears that low-quality "predatory publishers" are now using the well-known and trusted Editorial Manager software to try to make themselves appear more like legitimate scientific publications. So far, the company that runs Editorial Manager is effectively supporting this practice by declining to exercise due diligence in their business partnerships. I have a guest post up on "Retraction Watch" that gives all the details.

Sunday, February 12, 2017

Zen Walks

We're having unusually beautiful weather for February right now, so it's a good time for going out on zen walks. That's my name for a way that I walk when I want to go get in touch with myself, or when I really need to think something over.

In its essence, a zen walk is quite simple: put on your shoes, go outside, and begin walking. As you go, make no decisions about which way to go, but simply follow where your feet are taking you. At every intersection (and sometimes between them also), take the motions that feel the most natural in that moment. Let go of your image of where you might be going to, so that you do not just follow a habitual path, yet also let go of the image of avoiding your habitual paths, which also constrains your movements. Go, let go, and find out one step at a time where you are going.

Zen walking is without a goal, except for being there, and it brings me space to find out what I care about and what is on my mind. I am not a person to whom contentment and satisfaction come naturally, though there is surely enough in my life that I "should" be happy about. It is far too easy for me, though, to become caught up in "should" and "ought" and lists that I make for myself that generate unhappiness in their lack of completion. A zen walk is one of my tactics for letting myself re-discover that fact and finding my way back to which things I truly care about and why.

Friday, February 10, 2017

Protein Engineering Diagrams

We've got a new paper that's just been accepted, working toward extending the SBOL visual diagram language to be able to describe the engineering of proteins as well as DNA and RNA.  The core driving force behind this effort has been Sid Cox, who's done a good bit of work in the area and has had the courage to make this first surely-imperfect proposal, with a number of others of us helping critique, refine, and bend things towards compatibility and integration.

The idea behind the language is surprisingly simple: despite the ferocious complexity of how proteins fold and interact, when we engineer with proteins our actions can often be described much more simply. Proteins, particularly in complex eukaryotic organisms, are often quite modular, with specific domains controlling things like where they go in a cell, what they interact with, and how they decay. These are, in turn, laid out along an initial single line of amino acids (and encoded in DNA or RNA), and can often be recombined by mixing and matching these components. Doing that isn't simple, but explaining what you have done and why often can be fairly simple.

That's what our new diagram language aims for. Each protein in a system is represented by a line decorated with glyphs representing structured (oval) and unstructured (line) regions, membrane domains (zigzags), binding domains (open boxes), etc. With a brief glance, you can get a pretty good idea of what the protein or protein system is supposed to do and how it's supposed to do it.
Diagram for a two-protein design that provides light-inducible programmed localization to the cell membrane.
This is by no means a finished product, but it's a good solid start. Now that we've got a proposal, people can start critiquing it, and we can start working on various tweaks and philosophical debates necessary to get it integrated with the other diagram standards already in place, like SBOLv. This won't be fast, but it should hopefully produce a reasonable consensus on how to describe what's currently typically just shown as all sorts of random ad-hoc blobs.

If your institution permits, you can see the paper where it's been accepted at ACS Synthetic Biology, or you can read a preprint, and you can also play with the associated online diagram software.

Monday, January 09, 2017

Now witness the true power of measurement!

Today, one of my friends and colleagues sent me the following image. I am flattered, and notice that I am apparently picking up some kind of reputation, but I am entirely unsure on just how to interpret it. Dear readers, would you be so kind as to provide your own commentary?

Monday, December 26, 2016

Cooler than Magic

Our four-year old daughter doesn't believe in Santa Claus. We didn't push the Santa story, nor did we discourage it: we just let Santa be one of the many enjoyable cultural figures whose stories she knows, along with such other luminaries as Elsa and Anna, Durga, Peppa Pig, Jesus, Cinderella, Shiva, and Team Umizoomi. We've got a "no lies" policy in our parenting, though, so when some time ago she asked straight up if Santa Claus was real, the answer was simple: Santa is not real, but is a game that grownups and kids play, and once she knows the truth, she's playing on the grownup side and it would be very rude to spoil the game for other kids.

I'm certain that some people would say that we have done a terrible thing, stealing one of the pieces of magic from her life and shortening her childhood's period of innocence and wonder. I believe, however, that such concerns stem from a misunderstanding of what is so special about innocence and wonder. The innocence and wonder of children is tied up in many ways with their ignorance: you cannot experience wonder in exploring the geometry of a cardboard tube, for example, unless you are largely ignorant of geometry and cardboard tubes. I find that many people seem to confuse the ignorance, which is anything but valuable, with the innocence and wonder that happen to be associated with it in time.

As a parent, observing my child and other children, my current best understanding is that the importance of innocence is thinking and acting without feeling hemmed in and constrained by fears, and that the importance of wonder is the experience of how remarkable and marvelous our lives can be. It is much easier to achieve these states when we are ignorant, but we need not give them up merely because we become experienced. Rather, I think they are a critically important part of what makes life worth living.

Nor does knowing a truth prevent you from enjoying fiction. In my own experience, holding a very clear understanding of the distinction between fact and fiction can let you enjoy the fiction all the more because there is less need to be worried about whether it is true or how it may be affecting things. I even find it to be a good way to disempowering things that I am concerned about as a parent, like the Disney princess culture. If we try to hide from it or focus on criticism, that just gives it power as something that grownups are worried about. But if we embrace it, and acknowledge how fun the story is, but also help to remind and remember how it's just stories, and that stories are different from the real world, then it can draw the power out and turn literary criticism into a game that we can play together. Elsa is still an awesome queen with seriously cool ice magic, even if she'd be really sick if she was a real person with a waist that is so tiny.

The biggest difference, I find, in talking about fiction versus reality is that the "Why?" questions for fiction quickly ground out in questions of narrative structure. "In 'Moana', why did Te Fiti have her heart on the outside where Maui could steal it?" "They didn't give a reason. We can try to make up some reasons, but mostly it needed to be somewhere that he could steal it so that the story could happen." With reality, however, there is always something more, something outside, and ultimately things always ground out in an answer, and opportunity to look things up and learn, or, eventually, "That's a really good question, and we don't know the answer yet!"  And then maybe we can talk about how we might try to find out.

The reality of the world is so intricate, and its systematicity so remarkable that I find wonder is never very far from the surface. Driving through the fields a couple of days ago, I noticed a microwave relay tower and pointed it out, and we talked about communication. I love the great big scoops, posed on top of their rectangular spike of concrete, I love that microwaves interact with metal in such a way that their circuitry often ends up looking more like plumbing than wiring. I love that the waves themselves are inches wide, while an FM radio wave is about three times my daughter's height, and the light that I see is a bit less than a millimeter. I love that our civilization has erected concrete towers standing high across the plains like a high-tech semaphore network, relaying messages in a network little different in principle than moving goods in trucks or messengers riding horses in centuries past. There are thousands and thousands of such edifices out there, and many people have been involving in building them, bringing together on each of those thousands of sites a whole assemblage of heavy machinery, cranes, truckloads of electronic equipment, and so on. The more I think about it, the more wondrous that grey square lump of concrete with the funny metal scoops becomes.

Some of my wonder and joy, I think, comes from the training that I have received as a scientist. Most, however, does not need much specialization or knowledge to appreciate, just an open mind and a willingness to experience one's ignorance and look for answers. I would not say to embrace or celebrate ignorance, but to simply recognize it as a state of knowledge that one can choose what one wants to do with. A lot of people write themselves off from knowledge, saying that they just don't have the right head or the right training. I think that often this may come from a discomfort at being ignorant, and I am saddened by it. I think that we will all be better off, both as individuals and as citizens of our civilization, the more that we are able to embrace our innocence as seekers of knowledge and connoisseurs of the wonder of the world.

Later on Christmas day, as we looked through the window at the rain coming down outside, my daughter mentioned that her teacher had said that it would rain on Christmas. I asked her how she thought her teacher had known, and she told me her teacher must have read a weather forecast. And then we all talked as a family about how weather forecasts use satellites to look down from way above the Earth so that they can see what's going on over a very big distance, and see what weather is coming towards us over the next few days.

My daughter's eyes grew wide with wonder, and she said:  "That's even cooler than magic!"

I agree with her most strongly.