Thursday, January 29, 2009

Tuesday, January 27, 2009

Science and Policy Bootcamp - Day 2

Today my overwhelming feeling is, "Wow. How does government get anything done?" I've known that for years...but I guess I'd always thought that if I was there, things would change. How typically idealistic of me.

Today's focus was on creative innovation teams, and we started with the Department of Defense. I'll be the first to say that DOD makes me a bit nervous. I have family in the military, and while I do support soldiers that protect our country, it just has never felt right to accept the link between the DOD and science.

But, without the DOD, we wouldn't have interchangable manmade parts, assembly lines, electronics, semi-conductors, aviation, radar...the list goes on. But - we can realize that the DOD doesn't see their role as completely military. Many technologies that came from military funding serve very non-militaristic purposes now, and eschewing the importance of that kind of R&D is just naive.

Even so, the fact that economists like Vernon Ruttan (a University of Minnesota professor) even ask the question, "is war necessary for economic growth?" speaks to the role that military has in innovation. Do we need that kind of driving force, that challenge pervading our everyday work culture to actually accomplish things? The distinguishing factor between the military and the National Science Foundation is that promise of deliverables: "The country will be kept safe." versus the idea of "Yes - we'll learn some stuff." This is also known in the innovation world as utilizing a challenge model. And it works. During World War II, a group of engineers was brought to Los Alamos to assist with the Manhattan Project...but they weren't told why they were there, what they were doing, and only recieved vague information from their physics peers regarding what they were creating. Finally, Oppenheimer decides to override Washington's concerns about security, and tells that this project is attempting to build the atomic bomb, in a race to save human life. Productivity increases overnight, and things get done. But is there a way to do this without a doomsday prediction at your door?

Another point with the military is that it is effectively a "dictatorship." If top command sees the utility of a certain technology, there is instant adoption and implementation...there is effectively a built-in market for this new product. Now--turn this around and put it in the public sphere in the attempted legislation on fluorescent light bulbs and alternative energy. Instead of being praised for early adoption and efficiency, congress is accused of "turning socialist." Wait -- what? It's okay for national security, but not okay for other issues like energy independence...which is, oh shoot. National security.

In total, tthe hree main tenets to spur innovation are the capitol (money and physical equipment), people, and the organizational structure. Thus, the government can technically improve innovation simply by tweaking the manner in which it organizes these groups. The key to this group sort of organization materializes in DARPA (Defense Advanced Research Projects Agency) after the Sputnik embarrassment to American progress in 1958. Instead of dealing with three separate space agencies, Eisenhower decided to take away the space program from the military entities and hand them over to DARPA, until space responsibilities were handed over to NASA in 1960. However, this left DARPA free to focus on computing, and most of the early computer science departments (including MIT until a few years ago) were almost exclusively funded by DARPA.

To clarify - DARPA is not a specific physical place - it's colloquially known as "100 geniuses connected by a travel agent." One of the upsides to DARPA was the relatively flat heirarchy. This is something we talked about a lot today - how having only two levels makes for a much more even playing field, as well as easier means of communication, and a small enough work force to be truly effective. Interestingly enough, DARPA makes a point of contracting with both serious veterans of DOD work as well as newbies, for there is some serious benefit in involving an untrained eye and mind in on a project. (As an aside, it's odd thinking that someday I'm going to cross that border from newbie to veteran).

There was a huge problem during the Cuban Missile Crisis of "command and control" (communication between all branches of the military on a real time scale). One of DARPA's new assignments was to effectively create these connections. Ever heard of the internet? The thing that makes DARPA really great is that they saw the product, and went back to the necessary fundamentals to figure it out: they were interested in breakthrough technology and were okay with high risk operations.

We also talked about several other innovation groups: one of the first was Menlo Park in New Jersey, a research facility bounded by Thomas Edison to create the light bulb. They succeeded---but the more amazing part about the story is that they also made the leap to explaining electron theory, and building the entire infrastructure to power their new invention--utility companies, power plants...the scope of what inventing the light bulb actually involved was incredible. And they made pies together at two in the morning and sang songs. My kind of place.

Do egos ruin innovation? If you can't play well with others, should you get rid of them? There are arguments on both sides, but if your innovation system is based on groups, you're not going to have the same amount of group cooperativity of That is important, but the other option is to manage these particularly difficult scientists. Shockley, a researcher at Bell Labs, became known as the industry jerk for breaking up a collaboration at Bell Labs with semi-conductors, which effectively made Fairfield Semi-conductors and not AT&T the predominant semi-conductor manufactorer.

The story of Genentech was also surprising. Apparently the founders of the company met in a bar to talk about the genetic engineering revolution, and this meeting is in bronze in the lobby of Genentech in San Francisco. When you deal with biotech start up companies, there are a couple of different variables that keep you on your toes. First, the 1980 Bayh Doyle Act makes it much more difficult to give founding members stock options in a start up company (one reason that many scientists head abroad, where these options are still intact). Second, the FDA is a pain. And it takes forever...but what they DO is certify that a drug actually WORKS. That's a huge deal. Pharmaceuticals are the only field in which a product is certified to work correctly. Third, unlike the 25 years it took for internet to go from bench to homes, biologics can go from bench to medicine in eight years, a much smaller time period (which makes biotech startups a more viable platform for angel and venture capital).

A point was made to show the differences between MIT and Harvard: the former of which has a very meritocratic system (no honorary degrees), as well as the presence of immigrants in both the faculty and classrooms. The diversity of thought has always made MIT a very distinctive institution, and it is still unique among research universities for its collaborations between science, engineering, and industry.

The speaker today was David Goldston, the former Staff Director of the House Science Committee. He now writes a column for Nature magazine and teaches a course at Harvard. He spoke of his job on the House floor, as well as the strategy and manipulation involved in his day-to-day life. He is a real people person, and it is essential to his job to network and talk to people, persuading him that science matters.

One of his first points was to differentiate science for policy, and policy for science. Both are science policy, but their goals are completely different.

---Science for policy is the use of scientific discovery and innovation to drive policy-based decisions. For example, science for policy is using data on climate change to inform congress on specific actions that could be taken to alleviate the problem.

---Policy for science is how the government regulates science and controls science-based spending. For example, science for policy is setting the budget for different labs or types of science, as well as mandating the use of stem cells in research.

The thing to keep in mind in terms of science policy is "what does the country need?" And then within those restriction, what are the rules, regulations, and politics which allow for fulfilling this need?

For instance, an example he gave was the standards for lowering ozone concentrations in the air in 1997. According to the science, there is no threshold at which ozone is "safe." The rubric provided is a relationship between the level of ozone and the number of hospital admissions. So, when the bill got to the floor, the debate was on, "How many people can be admitted to the hospital?" No one wants to debate this, and there is no really scientific solution. That's where the policy comes in. And things get complicated.

He also commented on the climate issue, something he considers atypical in DC, for congress is debating a purely scientific question (is climate change real?), there is a majority scientific answer in place (not an answer by science), and the consensus in science didn't move the debate at all. The issue is now becoming that since the conservatives spent so much time in denial, they have shoot themselves in the foot in terms of defining the actual policy positions that will come out of this discussion. Even if Congress decides "Yes, climate change is real" they still need to determine how this will affect US policy in terms of energy consumption, biodiversity, environmental sustainability, etc...and that is going to be really challenging.

Another interesting thought to keep in mind is that members of congress are not chosen via merit. They are elected public officials, and may or may not feel that understanding science or knowing US economics is essential to their job. Fortunately, senators do have staff members to help bring them up to speed, but is this good enough?

Frankly, when hearing all of his stories, Congress reminds me of grade school. The interpersonal relationships seem very juvenile, with things changing based on what someone said in the elevator.

Apparently, when you actually visit with congresspeople, you have two jobs: convince them that this will help them become re-elected, and it will also bring money to their district. That made me kind of that all they think about? And legislation just takes a long time. It is tedious, yet also an critical part of a democracy.

I also asked him how he keeps up with the news: his recommendation for reading materials is the New York Times, the Washington Post, and the Wall Street Journal, as well as online sources (BBC) and NPR. Bills and memos are also available online, which is a resource that hasn't been around for too long, but it makes the process a lot more transparent.

All the better to get more familiar with the legislative process...

Monday, January 26, 2009

Science and Policy Bootcamp - Day 1

This week, I'm participating in an intense public policy and science course designed to be a first introduction to the history of science in America and abroad, and how economics supports and interacts with research and development. MIT is a school that really pushes for its students and scientists to interact with policy-makers, for they are a key part of the current method for acquiring funding and the means to pursue research. In general, MIT"s other agenda with its students is to teach the value of convincing anyone---absolutely anyone---the importance of what you do and that it MATTERS. This is a skill that isn't innate to all, and whether you are writing grants, talking with the public, or working as an educator, MIT will teach you to do this well. And that's probably one of the reasons it is so successful in science and technology, as well as other fields.

There is also an opportunity to visit Washington to lobby congress in the second week of April, which would be an amazing opportunity. (and the cherry blossoms!) I would be working mostly with the Massachusetts delegation of senators and representatives (John Kerry and Ted Kennedy), but I would also petition to meet with the Minnesota delegation (Amy Klobuchar and TBD).

[ Although - I might try and battle my way into Michele Bachman's office and sit her down for some serious tutoring on evolution: "there is a controversy among scientists about whether evolution is a fact or not...There are hundreds and hundreds of scientists, many of them holding Nobel Prizes, who believe in intelligent design." Right, Michelle. Name those many. And those hundreds. Then we'll talk. And maybe by the end, you'll understand what the concept of "theory" means in a scientific sense. (cited from a debate in St. Cloud in 2006.) ]

Regardless of what I do in Washington, this first day was full of all sorts of new and interesting things, some more related to science than others. The class was taught by the Director of the Massachusetts Institute of Technology's Washington, D.C. Office, Bill Bonvillian. He's an older gentleman, but he has had tremendous amounts of policy experience. He knows what he's talking about.

Our first order of business was really talking about what innovation means. Innovation can come in two forms: capitol (money, tools) or systemic (networking, allowing unified cooperation across fields). One of the big questions in this class is "How essential is the government's role in facilitating innovation?" Right now, the US system of science if industry (private sector), universities (funded by public research dollars and industry) and publicly funded research labs (think Bell Labs). The money and ideas that flow between these three areas isn't constant or even managed very effectively or efficiently. So--how do we do this? Should we try?

The argument in this class (and most overwhelmingly elsewhere) is that yes, the government should be involved. The point of contention is how. And how much.

Robert Solow
(an MIT prof who won the Nobel Prize in economics) - said the key to growth in both developed AND developing countries is research and innovation. But - he also said that this sort of growth is exogenous to the process, and isn't inside the economics of the system.

Paul Romer (a professor of economics teaching at Stanford) - is another important figure, and asserts that R&D is more complex: you need a real investment of people -- talented people. I completely agree. However, there is a lot of argument on how to best get these talented people. I would immediately say, "K-12 education is a mess. That's the best place to put money." However---Romer thinks that the best way is to reduce the dropout rate of engineering students at the college level.

There's also the very real problem of intellectual do you protect the inventor yet promote diffusion of knowledge and fuel scientific progress?

Another issue--who decides what is the "best" science to pursue? This is very much a value judgment. Way back in the day, people studied radiation instead of curing disease, and it led to the discovery of x-rays, and x-ray crystallography, a crucial technology to determine the structure of molecules, which lead to the discovery of DNA. Meaning, what is being researched will most certainly have far-reaching consequences, no matter what it looks like at first glance.

In another vein, why is so much money used to research drugs to cure adult onset diabetes and obesity when both are completely curable and preventable by a lifestyle change?

EDIT: It was pointed out to me that this is rather harsh. The big problem I have with all the money that goes to diabetes and obesity research is that it goes straight into Big Pharma. Why? Because Pharma can't make money off patients with rare genetic disorders. Instead, they can make money off the increasing number of obese and diabetic patients in this world. Granted, I think that these problems can be solved without drugs a great deal of the time but this REQUIRES a more supportive society and lots more nutritionists, exercise coaches, and incentives. It requires a large change in how American culture solves health problems. And then the money could go to those other diseases that often aren't supported because they mainly hit children that die young, or people in third world countries that can't pay for drugs. A win-win situation, to be sure.

Health care is already sucking up 20% of the total GDP...isn't prevention a good idea? Why does America have such an issue with legislating that sort of change? Or even offering greater incentives? There is a large connection between technology and sociology. The industrial revolution profoundly changed how life worked, more or less. So where are we now?

Science is also very dynamic, and there is a relationship between science and technology that goes both ways: things like electron microscopy enabled nanotechnology and further study of molecules, but the understanding of the basic science of atoms influenced the creation of better tools. It's a very mutual relationship. So - do we try to split up science and engineering? Do we pinhole the work professors do and accomplish?

Also - will competition work in a monopoly? We have so many different sectors of science, but is that the best way? We restrict access between these groups, but does this fuel competition in order to get things done, or does it do just the opposite?

There was also an interesting side discussion of the incentive of academia versus the money of industry. Why do I do what I do? For the money, obviously. There was talk of putting more obvious benefits into academia, but will that work?

Additionally, there is is the issue of relevance in terms of how the outside looks in and sees what scientists are attempting to do. The analogy was made is that science is like a monastery. We stay isolated from everyone else, write things down that only we can understand, and then throw our manuscripts over a wall. Then, a businessman comes along in a Cadillac, and he first must want to stop. Then he has to translate the foreign document, and understand what it is saying. Finally, he must know what to do with it will actually change things. It's an odd analogy, yet...I see his point. We don't have accurate means of communicating science to investors in many cases...or even to communicate between specific disciplines or across the public/private divide.

I also learned a bit more about the RadLab here at MIT - it's a fascinating story of how to get science done quickly and well. From the moment of getting the initial technology of microwave radar from the British, it took only 24 months to install fully functional radar systems in the entire American air fleet. That is astonishing.

All in all---wow. It was a complete overload of information, but hopefully it will help me become a bit more confident in the issues of science and policy. And yes- there are more questions than answers. Welcome to science.

In closing, to echo M. in a prior note, there was a student texting on his Blackberry throughout the entire lecture (keep in mind-today's class was five hours long). That is disrespectful. You know better. End of story. Watch your back, because next time you leave the room, I'm going to hide it.

Thursday, January 15, 2009

Mmmm...suckling pig!

One of the great things about being home is realizing that yes, while I don't have a TV at school, sometimes it is just nice to sit on the couch in the living room, turn on Food Network, and gasp at the beautiful food.

The particular episode of Iron Chef that was on that night was on suckling pig.


I'm not going to post a picture in the interest of not scaring away readers, yet as a scientist, I find the suckling pig a rather interesting specimen. First, I have dissected into the double digits of fetal pigs in my life as a student and teaching assistant, and I find it interesting to no end, every time I do it (even though, yes, they smell, and yes, I HATE touching the string that is always soaked in pig juice). And even now...I miss it. I miss being around people who are just as excited about cecum as I am. Instead, I have people who get their kicks from coding. Which is fine...I just miss biology majors.

And even the bio majors here don't have the same comprehensive anatomy/physiology-based curriculum I had in undergrad...I mean, I didn't take cell biology. Or molecular biology. Or molecular genetics. And that's the biology I am expected to know here. Instead, I find myself spouting random factoids in class about the histology slides in that paper we read, or talking about how respiration really works. And I really like that. I miss the part of my life that was teaching and talking to other students about cool awesome biology stuff.

Hence, once of my next projects (of the bazillion I have) is to try and create a K-12 learning module on malaria. Well, the first step is actually seeing what is out there...and if there isn't much, seeing what I can come up with or possible partners. Malaria is just such a complex issue that deserves a lot of thought, and it would be a great way to increase scientific literacy in the context of health, world issues, economics, culture, the environment...I could talk about it all day. In fact, it would be a REALLY cool job to do this for a living. Take a subject, customize for different grade levels, visit schools and perform these modules in an effort to teach something new and different.

Adults may decry the thought of getting everyone involved in these complicated issues and "not paying enough attention to test scores," but I maintain that by not providing opportunities which take advantage of and encourage creativity, we're doing our nation a grave disservice...the next generation of entrepreneurs, artists, and researchers won't have the breadth and ability to make changes happen.

Call me idealistic if you will, but I want to expect a great deal from the people around me, and I feel like my life should be spent enabling others to help them live up to that expectation. And the amazing thing is that this could come from working in public health, sustainability, research, a government job, teaching... No wonder I have no idea what I want to do for the rest of my life.

And this post started with suckling pig. Yes, yes it did. Oh boy.

Wednesday, January 14, 2009

Happy kitchen!

I was able to score a free kitchen stand thing off of the reuse listserve here at MIT about a week ago...and after de-rusting and WD-40ing, it is now installed in my kitchen and looks great! It is so nice to have some extra space!

Below is my kitchen/living area, starting from the front door and leading into the living room:

Friday, January 9, 2009

Recipe: Project Meat Glue

While I am awaiting the conversation with Jacquin about intellectual property (patent-related stuff), I thought I would mention that today was the first time I was in a "closed" meeting. In my entire life. The meeting was at the Broad Institute (so you know - it's said Brode, not Broad - I looked like an idiot the first time I said it, so...yes). That's the place responsible for the Human Genome Project (it's right across the street from where I work). Anyway, it was a meeting of a consortium for infectious diseases, and it talked about novel drug discovery for malaria. I don't know - it just strikes me as kind of interesting how much science can be hampered by IP...yes, it does protect people and their discoveries, but does it do the best for humanity? I'm torn.

Anyways--back to your regularly scheduled blog post:

Lab protocols are very similar to recipes, but as one of my fellow lab members pointed out, "You don't get to eat anything at the end."

-list of ingredients = cells, proteins, reagents

-cookware = equipment in the lab: all sorts of machines and incubators and such

-directions = protocol for doing the experiment

Much like cooking, if you are making something you have never made before (even if someone else gave you the exact recipe) you might have troubles the first time. Maybe it's the humidity. Or your cells weren't "happy" (industry slang for stressed and low on nutrients). Or maybe you added ingredients in the wrong order unintentionally. Either way, there is a lot you have to do before you can even get started in the lab, hence the fact that my "working in the lab" this week is actually me reading lots of papers, doing lots of internet searches, and preparing an introductory powerpoint presentation for a lab meeting in two weeks. This has to include a background, as well as things like specifics about what you are adding and doing.

For project meat glue, the first step is working out the ingredients, and that requires oodles of database searches, looking for exactly the right flavor of what I need...then deciding which equipment is best and going through with things. All with the help of the other folks in lab - in this case, when you are learning, there are never too many cooks in the kitchen. = recipe.

Boston Restaurant Guide

I'm not sure quite how to publish this one, but I think I will print as is, and edit in as I go, so it becomes a helpful restaurant guide).

Below are the restaurants where I have eaten here in Boston, as well as a bit about each of them:

Anna's Taqueria (MIT, various) - filling and cheap.

Au Bon Pain (Kendall, various) - kind of like Panera. Good but gets expensive...

Bartley's Burgers (Harvard Square) - all of their burgers are named after political figures--it's really cramped, so don't go with too many people. Sweet potato fries are yummy.

Bertucci's (Central Square and others) - the rolls are like CRACK. Otherwise, it's like Olive Garden but better food.

Blu (Downtown Crossings) - the meal I had in the cafe wasn't great, but the food in the restuarant is supposed to be's in the health club of a hotel, so it's not somewhere expected, but it has gotten great reviews

Cabot's (suburbs) - ice cream is better than the food...really elaborate and awesome death by chocolate creations!

Central Kitchen (Central Square) - great local food. Pricey. They used heirloom tomatoes that they had bought at the farmer's market a block away.

Cheers (Faneuil Hall) - overrated - but I'm glad I got to go with my mom and take a picture of her with her Cheers mug :)

Christina's Ice Cream (Inman Square) - bigger portions than Toscannini's, and both their sorbet and ice cream is wonderful. Bostonians are ice cream snobs, so most places here are quite good.

Daedalus (Harvard Square) - lovely rooftop garden. Wonderful salads.

Dim Sum (Chinatown) - go with someone who speaks Mandarin. Otherwise your experience just won't be as good.

East Coast Grill (Inman Square) - LOUD. but fantastic seafood...and the sangria is to die for.

El Pelon Taqueria (Fenway) - cheap and filling.

Emma's Pizza (Kendall) - deliciously quirky pizza. upscale and yummy

Excelsior (Boston Common) - really expensive, but great for Restaurant week - they even brought out a large piece of dark chocolate with "Happy Birthday, Bridget!" on it in delicate white icing, with a small candle molded to the plate with icing. Celebratory without obnoxious singing...loved it! Also, it was louder than most fancy restaurants are, and their wine cellar is awesome (you come through it on the elevator to the second floor where you eat)

Fire and Ice (Harvard Square) - "mongolian bbq-style" - For someone who has had, you know, semi-real Mongolian BBQ (thank you, Khans!), this was terribly bland for me. But the $10 all you can eat Monday night student deal really feeds college guys quite well

Flour Bakery (near South Station) - amazing sticky buns. Call ahead to reserve yours...they sell out quickly!

Four Burgers (Central Square) - sells beef, turkey, salmon, and veggie burgers, and you add but $10 a burger. I met the owner - super nice guy

Herrell's Ice Cream (Harvard Square) - it's in an old bank, so they painted the safe to be aquarium-esque! Very cute!

Kelly's Roast Beef (Revere Beach) - have the beef sandwich or the lobster roll. So good!

Koreana - (Prospect and Broadway in Cambridge) - good lunch specials $9ish

La Famiglia Giorgio (North End) - HUGE portions of pasta. And students get a 20% discount. Leave room for cannolis (basically, stuff yourself on bread, eat a couple bites, and bring the rest home...I had enough for three meals)

La Verdad (Fenway) - opened by a famous chef. Because he wanted to have a taco store. Bring friends and get the chips and guacamole. An order is $7 (as much as your burrito) but totally worth it. Oddly enough, guacamole tastes amazing with parmesean cheese.

Legal Seafood - (Kendall and others) - super expensive, but the seafood here is top shelf. I personally loved the crabcakes, but lobster is also delicious.

Miracle of Science (Central Square) - the menu is on the wall in a periodic table. You can tell you're near MIT really isn't that good. But the name is priceless.

Modern Pastry (North End) - beautiful cannolis. Have three.

Olive Tree - hello $2.85 falafel sandwich with lentil soup! Go early and be served by the owner's 13 year old daughter in plastic looney tunes flatware. Decor is priceless...wait, it all has prices on it. Even the donkey footstop.

Pizzeria Regina (North End) - people who own it can get kind of cranky...there is usually a line outside (they don't take reservations) - realllllly good pizza.

Pourhouse (Boston, near Boylston and Mass Ave) - half-price burgers on they cost $3. It's usually hard to find a table, and they have no one in charge of seating, so it's kind of a dog eat dog experience. If you're not up for smushed elbows or being pushy, don't go.

Punjabi Dhaba (Inman Square) - cute store with Bollywood playing while you wait. Best bang for your buck, and it's all served on these classy tin cafeteria trays. Make sure to get naan, and a lassi if you're feeling thirsty.

Rialto (Harvard Square) - absolutely amazing. Tuna tartare was beyond delicious - and while food there is pricey, it is doable for the $30 prie fixe meal during restaurant week.

Royal Bengal (Central Square) - good buffet

Sagra (Davis Square) - great Italian for a first date.

Shilimar of India (Central Square) - also a good lunch buffet

Sunset Bar and Grill - the best beer selection in Boston--reasonably priced flights as well. Food is good, too.

Toscannini's (Central Square and others) - mmm. I like ice cream. A lot.

Upper Crust (various) - excellent large slices of takeout pizza. Sometimes they have steak on their pizzas, but it's a lot of unconventional ingredients

Places I want to go:

Hungary Mother (Cambridge)

The Beehive (Boston)

Pho Republique (Boston)

Persephone (Boston)

Toro (Boston)

Plus many many more for restaurant can bet I'm saving money for it now!

Wednesday, January 7, 2009

The Transglutaminase Project - code name "Meat Glue"

Transglutaminase is an enzyme, which means that it is a protein that catalyzes the change of other molecules within a cell. There's actually quite a few neat facts involved with this enzyme:

-it was discovered in a study of blood clotting factors in 1968

-it is used by food chefs as a bonding agent for proteins

Ajinomoto Food Ingredients

Since this enzyme is a common one, it is isolated using a fermentation process, and you basically sprinkle it on different meats that you want to bond together. It's really popular in the "molecular gastronomy" field - the people that make nitrogen-frozen strawberries for desserts and use blow torches a lot.

-In patients with celiac, gluten comes into contact with transglutaminase and the enzyme modifies the gluten. This reaction causes an elevated immune response that is poorly understood, but the results are the synthesis of far too many antibodies that tell the body transglutaminase is toxic and must be destroyed. Thus, in celiac patients, they are lacking the ability to digest gluten, and the immune response causes inflammation in the digestive system which also hampers digestion as a whole, glutenacious or not.

-use as a surgical glue and tumor treatment is being investigated

So what does this have to do with malaria, you ask? Well...even I really don't know yet. But the really interesting part of this enzyme is that it has a drastic conformational change that occurs with the addition of calcium and a given substrate (think gluten as as example)

So...the best way that I found to think about these two enzymes is using the "Heads, Shoulders Knees and Toes" game. Red is the head, orange is the shoulders, green is the knees, blue is the toes. Thus, when the enzyme is in "closed" position, the head is really close to the toes, but in open conformation, they are really far away. This is about as dramatic a protein change can get.

What is even more important is how close the two ends of the protein are to one another. Many proteins are made of many different parts that are bonded together, but this one is basically one long string of amino acids, which in the above picture is represented by the ribbon and stringy things (fittingly, this is called a ribbon model).

The picture below is more 3D - you can see a bit more of how the molecules fit into space. You can also download a special program that will let you rotate this structure around in 3D space to try and better understand how it works.

However, with this picture, you can't where the protein begins and ends...which is why the lab is excited about this enzyme. If you look closely at the ribbon model, you can see that one end of the protein is actually really close to the other end of the protein when the enzyme is in the "closed" position and really far apart when they are in the open position.

There are some really interesting things we could do with this in terms of making it into a molecular tool, but first I have to do some background research into how the folding and unfolding actually works, as well as how to detect how it is working during an experiment, and if that can be done, see if I can control the movement with some small in, instead of the enzyme going back and forth between positions due to enzymatic activity, I would add a different non-related substrate and get it to do the same thing.

First, however, I have to map out some experiments to get things started.

The scientific process

Yesterday, I met with my PI (principle investigator) - he is the one who is officially in charge of the lab. Through a two hour Socratic-like meeting, we went over a possible problem for me to research and probe. As this is my first chance to dive in and really become immersed in a problem, I'd like to document how I get I plan experiments, and reagents, possible trouble-shooting, knowing lots of background...that sort of thing.

The first step is understanding the basics of our lab. Our goal is to build better and more effective molecular tools in order to help scientists understand organisms that don't follow the expected course. Generally, scientists use a suite of organisms from "least complex" to "most complex" in order to test hypotheses: e. coli, yeast, cells from mammals, C. elegans (a worm-like nematode), fruit flies, mice, rats, and humans. Yet, there are many organisms that don't act exactly like these systems that have been rigorously hacked: we have to engineer new ways to use what we know to come up with a way to solve what we don't know.

One of these organisms is Plasmodium falciparum, better known as the parasite that causes malaria (the red things above are red blood cells, and the crescent-looking shapes are the parasite). I'm going to be posting much more about malaria in the future, but for now it's most important to realize that malaria is a disease caused by a parasite we truly don't understand. They are a black box, and in the last thirty years of research, we've poked holes in this box, but due to the nature of the parasite, we haven't learned nearly enough to affect drug development or disease control of malaria.

Thus, the lab is focusing on engineering biological tools to help study malaria and other nonconventional organisms...which brings you to my project. Due to intellectual property concerns, I am going to have to be a bit vague, but if you ever have more specific questions, don't hesitate to ask.