Montclare Lab Group

#RealTimeProtEng

After months of seemingly endless grant writing and faculty obligations, I now have a short break where I can breathe until my next grant.  

Jin Montclare

Recognizing bias and making a difference

In light of International Women’s Day, I have decided to write about gender bias.  

I am a scientist/ engineer/ educator and I consider myself extremely fortunate to be at an academic institution leading a group of bright, creative, hard-working young scientists.  I firmly believe it is a privilege to mentor others and have a deep rooted responsibility to make sure I do my best to help my students develop into the best scientist that can be. Their future is dependent on their success and so my role as their mentor is extremely important.

I also happen to be female and I fully recognize the forms of discrimination out there in terms of gender, ethnicity and race.  While it unfortunately exists, it never entered my mind that I could engage in gender bias until I had my daughter.  I realized that in my daily interactions with her, my initial comments were on her physical appearance (ie-her cute outfit), which were followed by her actions (ie-her love of building with her blocks).  The subtle emphasis my daughter was receiving from me was that her appearance was more important than her actions.  

Once I realized my own subtle form of bias, I stopped.  I now consciously note her actions and make sure that is emphasized foremost in my daily interactions with her.  

From this experience, I am more diligent about recognizing subtle forms of gender bias.  They do exist and I urge you to self-reflect and make the change in your own actions.  I am more conscientious of my actions with my students and colleagues.  And importantly, I am expressing this as a form of support to other women and women in STEM fields.  Building support where we recognize bias is essential to increasing women and diversity.  So please share this perspective with others and make a difference.  

Jin Montclare 

What are your views on gender bias? 

Reflection on Hurricane Sandy—A Call for Solidarity

While I have always respected nature as a scientist/engineer, I never faced the wrath of nature until Sandy. As a scientist, my perspective has been to understand and exploit nature to engineer better systems. However after experiencing the hurricane that left us powerless on so many levels, I did what any scientist would do when an experiment failed or an unexpected result surfaced, I started the process of reflection and analysis. During this process, our apt had lost power, leaving us with no light, no heat, no water and no Internet. While it was unfortunate, I was thankful that my family was all right. However, I began to worry about my neighbors who were too old to walk up and down the stairs to get out out/get food, my students who were scattered throughout NY/NJ and all those seriously affected by Sandy. It was then I realized that reaching out was imperative and providing knowledge about the status of my building, my university, my lab was important to my neighbors, my colleagues, my students and my citizens. And so by word of mouth, phone calls, emails and social media, I did what I could to keep awareness and maintain a sense of stability in all the chaos. But more importantly, reach out to others and provide support as the only way we can overcome such natural disasters is by facing it together as a group. Like I always say to the scientists and engineers in my laboratory, in order to make advances in science, we must work together. In the wake of Sandy, in order to get back to normal, we must work together. We will be certain to regain power over this situation through solidarity. From Tuesday night’s election, our president stated, “We are an American family, and we rise and fall together as one people and as one nation.” So family, friends, colleagues, teachers and students reach out to one another and let us rise to the occasion and connect.

Jin Montclare

Programming Proteins with New Building Blocks

Proteins are essential components that allow us to exist.  If you look down at your hands, the surface or skin is comprised of various proteins.  And if you were able to look through your skin, there are a myriad of proteins that are working to sustain you.  

Now consider a situation in which deep inside your body, there is a tiny abnormal cell that contains an abnormal protein beginning to wreak havoc. Perhaps there would be a way to reprogram the protein so it can do the job it should do.

Well that is what we sought to do!   The most traditional way to reengineer proteins is to change their composition by making mutations, which will alter the amino acid building block sequence. However, we decided to take it up a notch and integrate new artificial building blocks into proteins.

To help you understand this, imagine that the building blocks of proteins are like opaque, colored Legos.  The protein would be represented as a pattern of those colored Legos in a certain shape or pattern.  If an artificial building block was represented as a transparent Lego, then the shaped protein would simply be comprised of them.

Getting back to our protein bearing the artificial building blocks….we were able to engineer a protein that contained different fluorinated amino acids (artificial building block).  We chose to investigate the histone acetyltransferase (HAT) protein.  The normal function of HAT is to activate genes by reacting with histones, which are the scaffolds that DNA are bound to in our cells.  In general our DNA are condensed with the histones, resulting in the X-like chromosome structure that you may be familiar with.  HATs can also activate other target proteins, which can lead to other biological events.  Thus, it can initiate parallel reactions in us. 

By playing molecular subterfuge on the cell machinery, we were able to coax cells to produce HATs with fluorinated amino acids. To our surprise one of the artificial HAT proteins changed its ability to specifically activate targets.  In our paper published in Molecular Biosystems (http://pubs.rsc.org/en/content/articlelanding/2011/mb/c1mb05148b), we observed that a particular fluorinated HAT showed exclusive activation of histone, knocking out its ability to activate another known protein target.  

Now why is this so exciting? Let us return to the initial situation where we need to reprogram a protein.  Our studies provide a route to address this and we are able to achieve this through a simple swap of opaque to transparent building blocks.   

Jin Montclare

In Aaron Dignan’s recent book, Game Frame, he provides a concise summary of the past century’s efforts to understand the motivating force behind games.  I couldn’t help musing, “are scientists motivated by game constructs as well?”  Are published manuscripts just another way to keep score (with impact factor providing a convenient score multiplier)?  Do games provide as much motivation for our work as it does a stock boy, day trader, or professional chef?  And finally, should games motivate as much as they do, particularly in the life sciences arena, in which others’ mortality could be at stake?

At first, the subtle commonalities of games and the scientific method may come as a shock to the non-gaming scientist.  For anyone who has ever played games requiring even a modicum of strategy, trial-and-error is the method of choice for learning.  Even with the limited control set of jumping and walking/running, as in the Super Mario Bros. game series, jumping across a chasm still requires the exploration of permutations of strategy: should I get a running start and then jump?; when should I release the jump button;? should I start off from a higher vantage point?  All of these are strategic decisions that, whether us gamers are cognizant of it or not, are informed by our experience from playing.  It should read: “educated-trial-and-error.”  They are, in effect, educated guesses – or hypotheses – as to how to solve a particular problem.

The notion of experience points (XP or EXP for you gaming readers) translates quite well into the life of graduate student/post-doc in the modern lab.  One can even imagine each stint in a different lab is the equivalent of conducting quests or “dungeoning” amongst members of a different guild; analogies pertaining to progression are evident.  However, do we as scientists view the practice of science in this light?  With menial jobs, employees typically overlay a gaming framework onto their simple tasks in order to motivate themselves to perform.  Do scientists do the same?  Enter gaming metrics.

Game metrics for grunts and newbies in science are simple: peer-reviewed journal publications with impact factor acting as optional multipliers, and (maybe) poster/oral presentations.  The idea of a PhD/Master’s thesis almost pales in comparison to something as quantifiable as the former.  Journal articles and presentations are inherently outlets to share one’s achievements with other fellow scientists.  Indeed, games in the proper sense are just catching up to this idea of social gaming frameworks.  Is it any wonder then that graduate students often find it laborious to push out a thesis?  In perhaps response to this, Magued Iskander, professor of civil engineering at Polytechnic Institute of NYU, will often ask, “how many pages have you written for your thesis?”  Some may argue that page number does not necessarily translate to quality of research, yet this is not the point of asking for such metrics.  It provides a quantifiable metric to track progress and motivate us to the next milestone, level, or chapter. 

On the professional level – as a PI of a research group – the game metrics are a little different.  This level of performance even comes with its own title, akin to the gold standards of “easy,” “medium,” and “hard.”  It’s called “tenure track.”  Publications still play a role, but additional associated metrics begin to affect gameplay.  Impact factor of published manuscript’s publications begin to behave as multipliers, with Nature and Science being the industry’s super uppercuts, and low impact factor journals being probing jabs.  Publication rate, on the yearly basis, is examined.  (Just recently our lab carried out a 6-hit combo in 2011.)  Acceleration of publishing, the 2^nd derivative, is also looked at by some of the more scrutinizing eyes.  The list could go on; as such, it’s not exactly caring solely about the science as a PI.  It’s about very quantifiable metrics that, in effect, turn the profession of science into a game in some respect.  Sure enough, there are plenty of PI’s offices with a white board that looks similar to a battlefield strategy. 

On the other hand, staunch academicians may claim, “This is no game!” and I wouldn’t blame them.  What happens in games, no matter how many measures we take to prevent it?  Answer: people cheat.  The motivating force of winning and the even stronger force for not losing/failing, and the perceptions of these ideas facilitated by gaming frameworks, can certainly drive people to cheat.  This can (and has) happen(ed) in several ways in scientific research: fudging data, withholding significant data sets, disobeying sensitive protocols, and even fabricating entire experiments and results.  This is particularly dangerous when it comes to clinical trials, prior to handing it off to the FDA.  But even with basic science research, public spending dollars are at stake.  Are we comfortable, as a society, donating money to efforts that may be tainted by our industry’s equivalent of Game Genie? (footnote: an invention in the late 1980’s allowing gamers to exploit the code of Nintendo games to offer such perks as unlimited lives, health and ammo)

I hope this post has at least provided a bit of a different perspective of scientific research to both the lay spectators, and the grunts and generals in the trenches.  The questions I’ve raised were as much a result of an introspective exercise as it was an attempt to redraw the canvas of the practice of science in America.  Hopefully, I’ve communicated how games can be a motivating force in the realm of scientific research, however subconscious it may present itself.  In addition, we must also be aware of the malicious effects of gaming constructs on our professional fields, science included.

The Network Blog

For the past six years, I have been creating and characterizing biomaterials. To be more specific, I work with materials made of proteins capable of assembling into unique structures. We have created proteins that possess two different segments: one which we call C that makes a molecular cylinder and another we name E that is structurally very different from the previous segment and possesses an ability to sense and respond to heat, pH and salts.

We pieced E and C in two different orientations, creating EC and CE and studied them. The most interesting thing that we discovered from our work is that EC block polymer has different functions from CE block polymer.

How is it possible that EC would not behave the same as CE as they are both comprised of the same segments you ask? Well, we think it may be due to the fact that the amino acids have different charities. Chirality means that the amino acids are not superimposable on their mirror image. Thus, orientation on each segment contains a specific chirality makes a difference.

After our discoveries, we decided to utilize the properties of our block polymers to make new hybrid biocomposites. We wanted to see how our soft biomaterials would behave in the presence of a rigid material (cellulose). Much to our surprise, we observed differences in their functionalities when they are mixed with cellulose. We were able to tune the function of our materials with the addition of other rigid materials found in nature.

So, here is a very brief description of what I’ve been doing my PhD. I am working in the lab because I love science, and I have always wanted to use my knowledge to improve the world. I am making my contribution to the world.

Jennifer Haghpanah