My Thesis in Three Minutes

Last week I did the Three Minute Thesis competition at Vanderbilt, which is basically a contest where graduate students present their research topic to a general audience in three minutes. You have to keep the science simple yet intriguing enough for the audience to want more. The organizers advertise it as great practice for elevator conversation but let’s be real, people are going to awkwardly ignore each other and check their phones in the elevator. Plus, a three minute elevator ride only happens in a skyscraper or an old, run-down building.

Anyways, I didn’t win it but I do want to share the most awesomest feedback I have ever gotten:

The Highest of Compliments!

Because of this, I’m still running high on my newfound motivation to do more science outreach. I’ve got a few good ideas so I will keep you posted on what comes out of it. I also remembered I need to catch up on COSMOS, which I hear is amazing thus far.

For any of you interested in learning more about the 3MT competition, please visit their website . For those of you interested in what my three minute thesis was, here’s the draft I made for my speech. The title is Dock It Like It’s Hot: Challenges of Modern Drug Discovery. I did my best to be funny but unfortunately on the day of, I had to go after a talk on childhood cancers.

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I’m a big Doctor Who fan so let’s time travel for a moment back to Elizabethan England, to the height of Shakespeare, the Renaissance, and crazy medical practices. If you had a sore throat, you might be prescribed slime from a garden snail. A toothache is treated with paste made from a mouse. Yuck! It’s no wonder these remedies didn’t work because doctors had little knowledge of how medicines worked. Fortunately, we’ve since learned a thing or two about both WHAT we should take and about HOW those drugs worked. Modern drug discovery though still has its own challenges, thanks to a few very large numbers.

It is estimated that there are 10^33 potential drugs out there. That’s 1 followed by 33 zeros! If we were to make a single pill for each of those drugs, the total would weigh as much as the sun.

Understanding how a particular drug works isn’t easy either. We know drugs act by binding to specific microscopic machinery in our body called proteins, similar to the way a key opens a particular lock. What makes it difficult is that there are 100,000 different types of proteins in our body. Imagine trying to figure out which lock a particular key opened in a building with 100,000 doors. What a nightmare. This makes it impossible for scientists to test everything by hand.

Enter the computer. The smart phone in your pocket is a computer capable of performing a billion calculations every second. There are supercomputers out there that are even faster. Why wouldn’t we harness this immense resource to help us find and understand the next generation of therapeutics?

Researchers have developed two separate set of computer software for drug discovery. Virtual screening help us filter down the near infinite list of possible drugs to a testable list of thousands. Molecular docking helps us understand how a specific drug unlocks a target protein.

My research focuses on bridging the gap between the two sides. I want to integrate our knowledge of WHAT drugs work from screening to help us figure out HOW they work through docking. For example, this morning I woke up with allergies and had to take a Claritin before coming here. Some of you might have had a similar experience but took an Allegra or a Benadryl instead. If we compare and contrast these drugs, we can gain insight into on how they work to treat the same symptoms. Let’s tackle the challenges of modern drug discovery by combining the WHAT question with the HOW question.

I like to leave you with some lyrics from the Snoop Dogg song that inspired the title of my presentation, “You should think about it, take a second. Matter fact, you should take four. “

March Madness (or Mayhem in case that’s copyrighted)

The theme song for this post is Queen’s Under Pressure

March was a pretty long month. I got a pair of new projects, both related to drug discovery for G-Protein Coupled Receptors. For my readers that don’t know what that is, roughly 50 percent of all drugs on the market right now work by binding to proteins in our body called GPCRs. These GPCRs are like the doorbells for our cells….you press the button, and things start happening. I also got a couple of proposals and mini-reviews to write now, so Microsoft Word has become my new best friend.

I’ve also picked up playing tennis and soccer more and more, which means watching more YouTube videos on learning how to play. Laugh all you want but they are actually a great resource for learning the basics of a new sport. It’s also a good place for learning kitchen skills or how to fix up your car. Just be careful because the internet has made everyone an expert on everything.

I obviously can’t get through a summary of March without talking about March Madness. My bracket didn’t do too well after the Sweet Sixteen. I had Virginia beating Michigan in the Championship and that’s out in a pair of nail-biters. As of today, a bracket where the high seed wins every time is 82 percentile on the NCAA website. That means most Americans would be better off not calling any upsets at all. I’m really thinking about using machine learning and neural networks to make a predictor for next year. I know other people have tried it but in research, you have got to believe you can do it better. My dream here is to present something like that at the MIT Sloan Sports Conference. I wouldn’t say no to $100,000 or however much you get for the top bracket.

That should wrap it up. I will try to get back to blogging more often and writing on some stuff besides updating my life, which unfortunately isn’t particularly exciting.

Back in Town and Back to Work

I decided on a random whim I’m going to attach a theme song to all my posts, and since I just got back from a week and a half in California, let’s go with: Boys Are Back In Town (Thin Lizzy)

The conferences were pretty awesome as was San Francisco of course. I talked enough about the Biophysical Society meeting since I was a guest blogger so you can read my posts here if you are interested. I had lunch/dinner with a number of old classmates and made some friends out of people that I previously only known by their username in our programming collaborations. I caught up on some craft beer at the 21st Amendment Brewery in San Francisco (highly recommended), and met my semi-annual quota of hole in the wall Mexican food. I also had Sushirrito, which is basically sushi, but in burrito form….but sushi, in a burrito…..I can’t emphasize it enough times, it was awesome (See picture).

Raw fish, avocados, spicy mayo...what more can I want?

Raw fish, avocados, spicy mayo…what more can I want?

I’m glad there are hipsters/creative people hard at work coming up with new ways to fuse my favorite foods from different cultures. Combining food groups, not just in those chain fusion restaurants, is just plain awesome. If you need another example, see bacon wrapped shrimp (which I plan on making in the near future).

Now that I’m back in Nashville, I have been mostly catching up on work and putting my luggage away. I did however, manage to get myself to the Vanderbilt Florida game. I had season tickets last year and this year but I never actually been to a game…a matchup with the #1 team seemed like a good opportunity. It was surprisingly less packed than I expected and I wished the student section were actually LOUD the entire game, but hey…at least I got some good seats. It was a really close game even though we lost; I think it was surprisingly more enjoyable and high energy than the football games.

Game on at Memorial Gym!

Game on at Memorial Gym!

Off to San Francisco!

Status

I’m off to San Francisco for a pair of conferences today through next Monday. I’m pretty darn excited for the food….I mean, for the conference. The first is the Biophysical Society National Meeting, for which I will be a guest blogger over on their blog (http://biophysicalsociety.wordpress.com/). The second is Rosetta Developer’s Meeting, which is essentially for the community of graduate students/post-docs that writes all the code for the software we work with. It’s a good balance between presentations on everything you can think of in studying cells/macromolecules to presentations on deciding what sort of log messages to write.

Graduate School: The Movie Soundtrack

I was sorting through my Spotify “Liked from Radio” playlist (it was getting out of hand) when I realized that a lot of my favorite lab jams could easily be about graduate school. There are at least a few lines in each song that could caption a PhD student’s life. Of course, Nostradamus and the Bible have taught us that you can pretty much interpret words to match anything given a large enough dataset. However, I still find myself singing along in my head (or out loud when it’s late at night) to the relevant lyrics. Besides, they are all good songs one way or another.

In other news, I will be off to the Biophysical Society National Meeting (and blogging from there!) soon…..more on this later. Here now then are my favorite songs from Graduate School: The Movie Soundtrack, also known as a list of songs I would love to parody:

PS: I would also love to hear your suggestions! Let me know if you got any good lab jams or songs that could be about grad school.

Blue Collar Man- Styx

My mother and father, my wife and my friends
I see them laugh in my face
But I’ve got the power, and I’ve got the will
I’m not a charity case
I’ll take those long nights, impossible odds
Keeping my eye to the keyhole
If it takes all that to be just what I am

Chances- Five for Fighting

Chances are when said and done
Who’ll be the lucky ones who make it all the way?

Chances are we’ll find a new equation
Chances roll away from me
Chances are all they hope to be

The Scientist- Coldplay

Nobody said it was easy
No one ever said it would be this hard
Oh, take me back to the start.

I was just guessing at numbers and figures
Pulling your puzzles apart
Questions of science, science and progress

Still Alive- Portal Video Game Soundtrack (Suggested by a colleague)

This was a triumph.
I’m making a note here: HUGE SUCCESS.
It’s hard to overstate my satisfaction.
Aperture Science
We do what we must
because we can.
For the good of all of us.

Peace of Mind- Boston

Now if you’re feelin’ kinda low ’bout the dues you’ve been paying
Future’s coming much too slow
And you wanna run but somehow you just keep on stayin’
Can’t decide on which way to go

Be Good To Yourself- Journey

Runnin’ out of self-control
Gettin’ close to an overload
Up against a no win situation
Shoulder to shoulder, push and shove
I’m hangin’ up my boxin’ gloves
I’m ready for a long vacation

Rocket Man- Elton John

And all this science, I don’t understand
It’s just my job five days a week

To wrap it up, I’m going to finish with a few parodies that are actually about grad school stuff:

Get Data – UCSD Neuroscience’s Parody of Get Lucky by Daft Punk 

Biotech Lab Life – PhDiddy

Fish Sex and the Book that Explains Everything

I just realized the title might be a little misleading but you’ll see what it’s about very soon. I wanted to throw in my two cent on the Bill Nye and Ken Ham debate, which you can watch over on DebateLIve if you missed it. Full disclosure: I am a graduate student in the biochemical sciences, and my real first name is Darwin. This means that I don’t believe in evolution. In fact, no one should have to believe in evolution, but everyone should understand why evolution is true and how it explains various aspects of the modern world.  

Overall, I thought the debate went very well and most of it was fairly entertaining. There were a lot of objections beforehand, particularly from scientists, about having the debate at all. In a way, it presents a platform for Ken Ham to present some misguided ideas and had the potential to confuse viewers about the “evolution controversy” as being 50:50 in the scientific community, when it really is more like 99.9999 to 0.0001. However, the debate ended up being a lot of re-hashing of old ideas for both sides. Bill Nye recounted the massive amount of evidence that we see, and Ken Ham tried to sell the idea of historical vs. observational science. I would give the victory to Bill Nye simply because he was able to promote future learning and present some key data that certain people might not have known about. The hard core people will not be swayed no matter what evidence you present, but there are a good number that are simply unaware of the available data and targeting them was a great idea. It helped that Ken Ham was promoting the extreme end of the spectrum in Young Earth Creationism, and not some sort of God-guided intelligent design idea that requires more scientific background to dispel.

I broke down some of my favorite (and least favorite) parts of the debate.

Best of Bill Nye:

Facts. The sheer amount of data he presented from all fields of science including geology, astronomy, and biology. His continued insistence on requesting examples of a provable hypothesis and his willingness to acknowledge what data would be necessary to disprove evolutionary theory. He also directly addressed the viewers and encourage scientifically literate education and voting for the future.

Worst of Bill Nye:

Jokes. It’s clear the science guy probably did not write the hilarious parts of the old TV show as he tossed in a few jokes that were just bizarre. The other thing was that he failed to address a few of the studies Ken Ham brought up. Some of those studies Ham brought up are commonly used by creationists and are easily refuted if you heard of them before.

Best of Ken Ham:

His favorite color is blue, I like blue too.

Worst of Ken Ham:

There were a lot of logical fallacies, especially appeals to authority from Ken Ham. Ham would show a video of a PhD scientist who would list off a few accomplishments and then say he does not believe in evolution. Of course, Ken Ham also states the views of a majority of scientists are not necessarily right. Furthermore, the whole idea of “you weren’t there so you don’t know” and “what’s the point of discovery if it’s gone when you die” are the two worst ideas for education.

Most Egregious Use of Logic:

Ken Ham, during a discussion of Noah’s Ark and whether or not Noah was skilled enough:

“Who said Noah couldn’t build a big boat? The Chinese and Egyptians built boats”

Most Awkward Example:

Bill Nye was discussing an example involving a minnow specie that can reproduce sexually or asexually. Instead of simply stating that, Bill Nye giggled and said that the minnows sometimes have:

“traditional fish sex” and sometimes “sex with itself”

Doesn’t it make you wonder what “kinky fish sex” entails (ha)?

My Favorite Moment:

During the audience question and answer phase, someone asked Bill Nye about the origins of the Big Bang and human consciousness. Although both are outside the purview of evolutionary theory, Bill Nye’s answer put a huge smile on my face:

“We don’t know!”

That ladies and gentlemen is why we do science…because frankly, we know very little about a lot of things. That very quote is the essence that drives our curiosity and leads to new discoveries/inventions. On the other hand, Ken Ham’s answer for all the big mysteries was of course:

“There’s a book out there that explains it”

Well gee, if I knew that, I would have looked at it to solve all of our mysteries instead of working on a PhD. One of my friends did point out that there is a book out there that explains a lot of the evolutionary questions brought up during the debate; we usually call it a high school biology textbook.

What’s Next? 

I’m looking forward to some good old Twitter comments and debates, since that obviously was not around during the Scopes monkey trial. I just hope that some student out there somewhere learned something today….that this thing called science, isn’t just a bunch of magic tricks and a black box. It’s a wonderful network of knowledge that explains the world we live in.

What are your thoughts on the debate or the education controversy in general?

Random Statistics: Super Bowl Edition

It’s a well-documented fact that 76 percent of statistics are made up on the spot. Actually, the number is more like 29 percent, the remaining are coincidences since there are bound to be some patterns in a world full of numbers. As some of you might know, my favorite alternate career choice should science fail me is sports statistics. I would enjoy being the statistician for NFL broadcasts that comes up with the factoid that some mediocre QB actually leads the NFL in passer rating when throwing outside the pocket in a 3 WRs set on 3rd down while trailing in the 4th quarter. Any time you can put up numbers that shows whoever the Browns have in as QB is better than Peyton Manning is an impressive accomplishment for your resume.

Speaking of Manning, the Super Bowl is this week! I hope it’s a snowy affair where the Manning gets tossed around by the Seahawks defense (as a Ravens fan, I can’t root for Manning thanks to his days with the Colts). I’ll be enjoying the game on Sunday the way it was meant to be enjoyed…with an excess of food. In the mean time though, here are some of my favorite random Super Bowl facts and statistics:

Food:
8,000,000: Pounds of guacamole consumed on Super Bowl Sunday
14,500: Tons of tortilla chips to go along with the guacamole
40: Approximate ounces I am responsible for

Super Bowl History:
10: Number of different NFC starting QBs in the past 11 Super Bowls
4: Number of different AFC starting QBs in the past 11 Super Bowls

10-8: The record of the #1 Offensive team in 18 Super Bowl appearances
12-3: The record of the #1 Defensive team in 15 Super Bowl appearances
1990: The last time the #1 Offense met the #1 Defense in the Super Bowl, the Giants Defense won over the Bills Offense

8-2: Madden (the EA Sports game) track record for predicting Super Bowl winners. It predicted the Broncos to win in overtime this year.

8-1: Record of team wearing white jerseys in the Super Bowl (maybe this year it will help camouflage the Seahawks in the snow)

4: The NFC West’s Super Bowl losing streak starting with the Rams, then Seahawks, then Cardinals, then Niners.

Betting:
99,000,000: Dollar amount bet on the Super Bowl in Vegas last year. This year you can bet on everything from opening coin toss (Dumbest bet ever) to number of times Omaha will be called.

91%: Vegas oddsmakers’ overall win rate over the last 23 Super Bowls.

33%: Percentage of games in the past 8 years that would have been won by 0-0, 3-0 or 7-0 in the Squares game (where you guess the ones digits of the final score for both teams)