The next phase: Into the lab

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December 21, 2016

Max Tan

Now… where were we? (Disclaimer: you might want to read the prequel to this article first.)

Your interest in spider silks has now evolved into an almost-unhealthy obsession. You ‘ve spent practically every waking hour for the past month reading articles at a rate that would worry any mother. You have befriended words such as “aciniform”, “major ampullate” and “MaSp1”. Where your friends simply see a cobweb, you see a mosaic of silks with different sequences and physical properties. Words on papers can no longer satisfy that unbearable itch that needs to be scratched: you need to test your hypothesis. You need a lab…

Finding master Yoda

Before stepping into any lab to test out your hypothesis, you’ll need to find a “master Yoda” who will take you up on your project – a Principal Investigator (PI). For all intents and purposes, your PI will be both your boss and your mentor through the course of your project. Seeing as to how you are merely a young padawan fresh off the boat, approaching a PI suitable for your learning is more important than approaching one who is illustrious but incompatible with you. That being said, here are some types of PIs that are often discussed at the dinner table:

The slave-driver: As the title suggests, this PI wants things done quickly and efficiently. If your PI so happens to be of this variant, don’t be surprised if you find yourself spending every free time you have either at the lab or reading papers. Though harsh, your PI is actually pushing you to your limit and out of your comfort zone, showing you what research life can be all about. This type of PI might be more suitable for the less-disciplined.
Mr nice guy: This PI is everyone’s dream work partner: generous, caring and pretty laid back. He is the popular guy in the faculty and his name is synonymous with the sentence “oh he’s very nice” (duh). His nice demeanor is often taken advantage of and can result in the ill-disciplined missing deadlines due to the general relax-ness of the working environment. Unlike “the slave-driver”, Mr nice guy might be more suited for somebody who is able to manage his time well.

Figure 1: The nine types of PIs as illustrated in The NIH Catalyst.

Eyes on the prize: “Do it however you think is correct. Just produce results.” This PI prioritizes the end result more than the process, leaving the uninitiated often clueless as to how to proceed with the project. This PI might be a better fit for the seasoned researcher hoping to make it big in his field rather than one who is just learning the ropes (aka you).

Evidently, these classifications are sweeping generalizations but are able to provide an inkling of truth to the current situation. Take your time in researching the PIs by asking your peers or grad students who might have worked with them before. Only they will be able to paint a good picture of what to expect while working under a specific PI.

The pitch

Here comes the part that will set the course for your entire project. Having found your ideal PI, you now need to sell your idea and convince your PI why your project is worth taking up. This can end in a few ways:

Your PI accepts your idea and decides to take you in. (Good. No problems here!)
Your PI rejects your idea. You can:
- Suggest a new idea that is related to the subject that you are interested in.
- Be willing to take on a project as recommended by the PI.
- Find a new PI that is willing to take on your idea.
Your PI does not have any vacancy for another student. (What can you do about it? Find a new PI.)

Sadly, while option 2 occurs most frequently, this does not mean that your idea is bad. It might just mean that your PI's goals are not congruent to yours. To that, I recommend taking a breather and don’t be pressured into accepting a project just because you need one. Evaluate the pros and cons and offer to get back to your PI the next day after thinking it through. Regardless of option, you must be certain that the project you will be working on is able to capture your attention for a sustained period of time. This will be important when you find yourself in the lab at ungodly hours setting up reactions or reagents.

Learning the ropes

As you first enter the research lab, soak in the virgin experience with every step you take towards your workbench. The soft whine of the fume hood. The chicken soup-smell of the LB broth. These sensory cues can hint at what is to be expected in the lab.

At your workbench, you are greeted with an unfamiliar face. This person is your mentor who will be guiding you throughout your time in your lab. As a start, your mentor will walk you through on the safety requirements and settings of the curious-looking machines that you will be working with in the not-so-distant future. Take this time to WRITE down any important pointers pertaining to the machine specifications (ie what is the usual working temperature) and question the rationale for each setting. I emphasize WRITE as I personally have the bad habit of thinking “there’s no way I’ll forget this” only to have myself forget it half an hour later. Technical stuff aside, try to learn the lab etiquette and culture during your first walkabout. You’ll never know when you’ll need the help of your fellow lab members.

On to the fun stuff

Before we begin on the experimental part of it all, here is a public service announcement: GET A LOG BOOK AND LOG EVERYTHING DOWN. Messed about with the temperature? Log it down. Got fed up with logging the experiment and threw everything together? Log it down. To quote Adam from Mythbusters: “Remember kids, the only difference between science and screwing around is writing it down.” You’ll never know when an experiment can turn out successfully or when you’ll need to troubleshoot a simple task like mixing salt with water (Take it from me. It has happened.).

Figure 2: Wise words to live by.

Regardless whether your experimental procedure was a hand-me-down from past students or a completely novel one, it pays to continue your readings into the field. While you’ll soon realize that experimentation is pretty different from theory, don’t stop reading. This can help in understanding why certain steps are done and will allow you to make modifications to your procedure. Ultimately keep in mind that as a scientist, be systematic with your modifications instead of simply changing variables at random. This process can be slow and tedious but it’ll help tremendously later on for trend-spotting.

Finally, preserve a sense of child-like wonder during your time in the lab. Be fascinated at that square crystal of sodium chloride or that little speck of dust (which was supposed to be silk) floating around in the test tube. You are now walking in the footsteps of many great scientists – being in the lab.

(Tip: Book any equipment you require well in advance. Plan your experiments well and have a contingency plan for any possible problems. Fix a date on when to end lab-work to work on your report so you don’t get carried away. Again, if you fail to plan you plan to fail.)

Negative results are still results

After months of preparing the silk protein and subjecting it to countless reagents, you find yourself growing more frustrated. WORK DAMN IT WORK! But it just doesn’t. At this point I can only offer the well-worn words of encouragement and point out the well-hated phrase “Negative results are still results”. While those words uttered in that sequence may appear as a mockery to all the hard work you’ve done up till now, believe me when I say it’s much better to have consistent, systematic failures than random, unpredictable successes (This will come up again later). Push on. The experiment is not over till you say it is.

Figure 3: a) Failure. b) Failure. c) Failure… sensing a theme here?

That moment when...

It is that one moment that every scientist lives for. To simply call it the “eureka” moment would be a major downplay of what it really feels like. For me it came in the form of a seemingly insignificant response: the liquid did not flow as I tilted the test tube, indicating successful gelation of the silk protein. It might appear unremarkable to the layman but to you it is the culmination of all the efforts that you have put in for the past four months. This successful experiment has affirmed your belief in science, allowing you to walk around for the next week or two with confidence that for that one moment, you knew something that the rest of the world did not.

Then you realize: you have not done a repeat. What if the result was a fluke…? And so, you spend the next night sleepless…

Figure 4: The picture of success.

Crunching the numbers

After countless hours of whining, cursing, crying and swearing yourself off the topic all together (occurring in order), you find that your time in the lab is almost up. You’ve (hopefully) collected all the data you need and all that’s left is just crunching the numbers. A cold grip stills your heart after poring through a library’s worth of numbers and analyzing a museum’s load of microscope photographs. The numbers add up and your t-test all point to the same heart-stopping conclusion: insufficient evidence to reject the null hypothesis in favor of the alternate hypothesis. Seeing as to how you don’t have the time to carry on with lab-work, my advice is to face the results with confidence and report it as it is. Don’t attempt to cherry-pick your results or engage in word-play to report your results as positive on a technicality; It is obvious to any potential reader and it will get tiring trying to keep up with the web of lies (see what I did there? Spider pun.). Instead, aim to suggest why you obtained your results and what improvements or alternative hypotheses could be tested in light of the results you have obtained.

The bottom line is that science is an impartial field – if the numbers say that it doesn’t work, it doesn’t work. Being uncompromising on this quality allows science to progress and prevents you from slipping down the slippery slope of deception and results-forging.

The poster

Unlike the report, the poster is a dumbed-down version meant to convey to your audience the wonder that is your project. Remove from your mind any scientific posters fraught with words or littered with graphs of little meaning. Instead, think of what makes a good movie poster: the title of the movie, the stars of the movie and a clue as to what the movie is about. Don’t be afraid to substitute entire sections with schematic diagrams or write in point form. This will allow the reader to easily enumerate your objectives or results, giving them a clearer picture as to what you have done. Bottom line: Show. Don’t tell.

Figure 5: So sad but so true.

Wait. That’s the end?

For fear of sounding like a broken record, what carries on from here would be a close approximation to the last three sections (This is it, Read, re-write. Read, re-write and Letting go) found in the prequel. The process of research, as you may have well known, has been fraught with pain and anguish. Now that you are at home reading this without the sharp smell of ethanol or annoying buzz of the sonicator you realize how tranquil life can possibly be… And you hate it.

And so, you set off again to relive that one moment when that liquid would not flow.