Applied Science

There is a big push in the university systems in the United States to develop research programs emphasizing Applied Science. Applied Science (AS from here on out) is one of the more recent buzzwords that you're likely to hear from administrators at universities, especially those that do not have colleges or schools of engineering. Applied Science, roughly, is the application of basic scientific principles to real-world problems and challenges. In comparison to basic science, it seeks to solve a tangible problem that directly affects the human condition, rather than studying the basic workings of the universe. In the university setting, AS differs from typical R&D in the corporate world as it tends to develop products that are not ready for production or sale, but could be taken over by a company and refined. The current emphasis on AS is due to a number of different factors:

1. The decline in research done by corporations. Ask someone over the age of 60 who is an engineer, physicist, or chemist about Bell Laboratories. I don't have the time or space to discuss Bell Labs and the innovations is produced (there's Wikipedia for that). Suffice it to say that, in its heyday, Bell Labs was the place for applied science research (as well as some more basic research). However, today's corporate world does not value AS enough to fund it as it did before. As a result, there is a niche that has opened up, and universities are rushing to fill it.
2. The change in US Federal funding. As the economy goes, so goes federal funding of research. In addition to shrinking research budgets, granting agencies tend to favor proposals that closely address a specific problem (a disease, a missing technology, etc.) rather than a gap in our knowledge. These two factors have decreased the funding available for traditional, basic research, disincentivizing it.
3. The search for new funding sources. Universities (especially public ones) are suffering economically due to decreased state and federal funding. Patents for products or processes developed through AS can be very lucrative (see FSU and taxol).

The move to AS by many universities will be interesting to watch. Schools with well-developed Materials Science, Engineering, and Technology programs will find increased competition for federal funds. Universities that have traditionally focused on basic science will have to strike a balance between all basic or all AS. While this is a good move overall, I fear that many universities are jumping into AS too quickly and with too much abandon, to the detriment of basic science. We still need basic science research to feed ideas for AS, but if universities start to weaken or abandon basic science programs, we will likely see a dramatic decrease in innovation and technological advancement 20 to 30 years in the future.

Storytelling

I am not a good storyteller.  I never have been.  Ask my brothers.  I'm the worst storyteller in the bunch.  Ask my friends.  I can pass along information with the best of them, but ask me to tell you a story and I'll likely leave you disappointed.  It hasn't stopped me from trying, though.

Storytelling is an important part of the human experience, anthropologists tell us.  Oral tradition played a huge role in the forming and defining of cultures.  Only recently have we seen a decline in the importance of oral tradition in terms of defining a culture (due to the rampant increase in literacy and the availability of reading material).  So while storytellers in the traditional sense are declining in popularity, we are still drawn as a people to stories.  It’s why the Star Trek, Star Wars, Lord of the Rings, and the Narnia franchises are running strong and why the Transformers movies have become a bit of a joke.  It’s why soap operas have lasted so long.  It’s why M. Night evoked first praise and the later revulsion.  It explains why Rick Reilly can write great features and terrible features.  It’s even why we watch reality television (compelling characters and the excitement of the unpredictable).

Important note here: Proper storytelling must involve a strong grasp on the storytelling medium.  It’s why movie adaptations of novels are radically different.  Thus, while the basics of good storytelling are important across the board, the best storytellers know the strength and limitations of the medium they use.

So why am I telling you that I am a terrible storyteller?  It’s because in the past weeks, I’ve noticed that my colleagues exhibit varying degrees of storytelling ability.  In the summer, fellow graduate students give half-hour Power Point talks about their research.  You may think that, as a scientist, I should be exited and enthralled to listen to new findings, techniques, etc.  And I was.  However, after years of listening to talks, the excitement wears off.  I find that I now pay closer attention (read: stay awake and alert) to talks that either deal directly with my research OR are well-told stories.  I also suspect that this phenomenon holds true in most, if not all, professions.


The reason I say all of this is to encourage everyone reading to become a better storyteller.  Find a way to practice, whether it is making up a story to tell your kids before bedtime, making videos or podcasts, writing a blog, or just practicing presenting something you read.  Great storytellers are not only more likely to be successful, but enrich the lives of the people around them.

Science Fights!

So it's been a month and a half since I last blogged.  Way too long.  Where will I get my writing practice?  And where will you get thought-provoking material to help you make it through the day?  Well, enough of that, we're back to blogging!

Today's topic is "Science Fights," or, as the scientific community prefers, scientific debate.  Scientific debate can take place anywhere at anytime between two scientists, but is most frequently observed after one scientist gives a talk, presenting his hypotheses and data.  Such was the case for the science fight I witnessed today. 

This science fight took place at a departmental seminar between two professors.  And to be fair, the "fight" was much more of a debate than a real fight.  One professor asked his question (in a way that was sufficiently amicable and respectful, though not overly so) and the speaker (another professor) replied with his answer (which was not condescending, but was not full of understanding and compassion).  The debate continued back and forth for a while, as each professor worked their way through the semantics of the other and tried to convince the other of their correctness.  At the end of the discussion, I don't think either side was convinced by the other, but their points had been made.

...and this is all fine.  It is standard fare for a scientific debate.  The reason I want to bring it up today is twofold.  First, I want to discuss the feeling of awkwardness that many of the grad students likely felt, and the second is to discuss what I find to be more and more interesting, the personalities that make up the scientific community.

First, the awkwardness.  Why did this "fight" feel so awkward?  If it hadn't I wouldn't have labeled it a fight.  Part of it was the combination of the difficulty each professor had communicating with each other at first (semantics, etc.) and I think the rest of it came from having two respected individuals (in their fields) arguing over something.  This may be akin to the first time a child sees his parents argue over something.  It's a little unsettling.  And that can't be helped.  But should it be unsettling now?  Should I (or any scientist at that point) have even felt awkward?

This leads into our second topic, the personalities of the scientific community.  I think scientists, especially in recent years, have made an attempt to create the appearance that all personalities are welcome in the scientific community (I'm not counting laziness, dishonesty, etc. as personalities here).  However, it seems that some personalities are either more dominant or successful than others.  This is where I'd like your input.  I would posit that people who are competitive, confrontational, and somewhat obsessive tend to be over-represented in the scientific community.  Or, if they are not, they seem to be more active/visible.  What do you think?  Am I right?  Do these people make better scientists?

Let me know what you think.  I know I said I would have a video blog post, and I will have one before May.  If you have suggestions for a topic, please comment and let me know!

Christmas Letters

Hey everyone!  I haven't found a particularly compelling article to discuss in a while, so I'll be talking about Christmas Letters.  I tired writing my first Christmas letter for my wife and I, as this will be our first Christmas as a married couple.  It was a tough balance, I thought, between being entertaining and informative.  Anyway, I figured I'd ask my loyal readers what you want in a Christmas Letter.  Should it be honest?  Should it be funny?  Should it be informative?  Or would you rather just have a picture?  What would make the perfect Christmas letter?  Thanks for the input!

Kamikaze Protein???

Today I will review an article that I really enjoyed reading.  However, before we get to the article, I want to give you the backstory to how I came to read it.  It started on a regular lab day.  One of my friends posted a news article on Google Buzz that discussed this paper.  Of course, the news article heralded this paper as ushering in a cure for the common cold in a matter of a decade.  This was intriguing enough (and so difficult to believe) that I decided to read the article and formulate my own opinion.  After reading the article, I was thoroughly impressed by the science and the findings in the paper, and thoroughly disappointed in how over-hyped the news article was.  In my disappointment (and in my quest to generate even more followers), I tried to find a way to write about this article in a way that is 1.) Honest, 2.) Exciting, and 3.) Easy to follow.  The following is the final product of my labors.  I'll let you judge it.

The paper I'll be discussing, Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21), is currently free to read, so if you don't have access to PNAS through a university, you can still read it!  How awesome is that!  Anyway, in this paper, Mallery, McEwan, and Bidgood (three first authors) discuss a protein, TRIM21 and its role in immunity.  Now, before we can get into the details of the paper, we need a quick reminder of how our immune system works.  The immune system responds to pathogens (disease-causing organisms) in two ways.  First, there is a general recruitment of immune cells to the site of cellular damage.  This process is why your finger turns red when you poke it with a pin.  The second half of the immune system is what confers immunity and prevents you from catching the same disease twice (a la chicken pox).  This system uses proteins called antibodies.  Each antibody is designed to recognize a particular part of a pathogen and will bind to it, signaling for other immune cells to come and destroy the pathogen.

Viruses (which cause AIDS, the cold, the flu, hepatitis, and many other diseases) are pathogens that must enter a human cell and incorporate their genetic material into the cell.  In doing this, they hijack the cell and force it to make copies of the virus, which then go on to infect other cells and other people.  It was thought that, once a virus entered a cell, that the cell was pretty much a lost cause and should be killed by immune cells, sacrificing one cell for the good of the body.  However, this paper changes this line of thought completely.  For those of you not in science, this is a HUGE shift in thinking, and may very well be Nobel-prize-worthy.

Anyway, let's discuss this paper and its paradigm shifting discovery.  The researchers here showed that TRIM21 is a protein that, when expressed in cells at high enough levels, will prevent the spread of virus in cells in a dish, if the viruses are coated first with antibodies.  There are no immune cells present in this experiment, meaning that the eradication of the virus is being accomplished by plain, ordinary cells.  The researchers then go on to prove that TRIM21 binds to the constant part of the human antibody (meaning that it recognizes ALL host antibodies). 

What happens from here is a little less clear, though very exciting.  TRIM21 is an E3 ubiquitin ligase.  Ubiquitin ligases attach the protein ubiquitin to themselves or other proteins as a way to send the protein to the proteasome (where the protein is destroyed).  NOTE:  This is a very simplified and slightly inaccurate description, but it will suffice for the topic of this article.  It looks like TRIM21 ubiquitinates itself, targeting itself to the proteasome.  Because it is attached to the antibody which is attached to the virus, these both get dragged into the proteasome.  Thus TRIM21 is now the protein equivalent of a kamikaze pilot.  While the evidence for this is not strong enough to be confident that this is really how it works, the available evidence points in this direction.

All in all, this is an interesting paper with great science.  However, the assumption that this will quickly lead to a cure for the cold is somewhat misguided.  Antibody recognition of the virus is critical for the success of TRIM21-mediated viral destruction.  The cold virus is tricky, though, as it mutates frequently, making it difficult for antibodies to keep up with the virus.  Still, the  discovery is intriguing and changes our view of how immunity works.

All right.  Stay tuned for more posts!  Your homework is to post the popular-culture equivalent to TRIM21 (from film, literature, tv, video games, etc.)  I'm looking forward to your answers!