by Youssef M. Abdelmaksoud, iGEM 2021 Ambassador to Africa

Attending the closing ceremony of the iGEM 2019 competition in our team CU uniform.

On that day, we nearly burst into tears!

It was just over a year ago, the 360 teams were all crossing their fingers as the results of the international Genetically Engineered Machines (iGEM) 2019 competition were about to be announced. We were on the second floor of the auditorium, staring at the enormous screen, when we saw our team name on it. We got a bronze medal!

From day one, our aim was a gold medal. We failed to achieve that goal. Our team encountered a myriad of both unforeseen and expected obstacles, we even dedicated a section of our presentation to talk about them. But another side of the story was never spoken of: The mistakes we committed.

It's no easy task talking about failures or blunders, even within the scientific community, a field wherein failure is a feature and not a bug. So, as assumed, writing this article was not an easy assignment.

Ah! Do not expect a plot twist! This is a classic failure story(ies), a cry over wasted opportunities, and a prayer to have a chance to try over, hopefully avoiding committing the same mistakes.

The Expectations Trap

In our quest to tackle the water shortage problem, we wanted to engineer microbes to collect salts from salty water, and voila! Freshwater!

We started with what we, being so naïve at the time, thought was a simple and straightforward aim: a fully functional small-scale prototype of our Biodesalination station! We wanted to go to Boston with a bottle of seawater, and an empty cup to fill with the resulting water that is fresh, potable, and totally-safe-to-drink-yet-no-one-would-be-allowed-to-touch-just-because-of-iGEM-safety-precautions; and show that to everybody. Needless to say, we did not bring any seawater-filled bottles; and no, the airport's security not allowing liquids on planes had nothing to do with that…

We failed to set reasonable and realistic goals, we noticed how this is holding us back and adjusted our aims, pared them down, and focused instead on short term objectives regarding lab work, fundraising, and other aspects of the project without forgetting that big picture. This realization and adjustment happened relatively early. Still, valuable time had already been lost chasing an impracticable dream.

Proposals are meant to be visionary and ambitious. The goals, however, should be plausible and, more importantly, measurable.

The chassis: 404

To collect the salts from water, we decided to work with a salt-loving yeast; the chosen one was Debaryomyces hansenii. A thorough literature search led us to that choice, and right away we started searching for a way to get our hands on it. Long story short, we failed. We did not find that yeast; or when we did, it was either too costly for us to order (even before accounting for customs and shipping fees), or in another case, the institute we ordered it from failed to prepare an active culture of it, meaning that they had dead yeast in their collection.

Okay. Not so much to blame ourselves. Our next reasonable move would have been working with Saccharomyces cerevisiae, an established model organism in Genetic Engineering and Synthetic Biology, but we thought we had a better plan. We decided to isolate the yeast from seawater. That could be a stand-alone project, but we foolishly assumed otherwise. It'll be a small side project.

We ended up getting some interesting data, found two halophilic strains of yeast related to our target (D. hansenii), sequenced them, and tested their tolerance towards salts. But this took us away from our goal. We spent a substantial amount of time and energy on this side hustle, planning, preparing growth media (we had to try a variety of them), culturing and subculturing, sequencing, and interpreting data, and of course, troubleshooting (lots of troubleshooting)!

We learned the hard way not to reinvent the wheel and to enjoy a good shortcut when we recognize one. In our defense, reinventing the wheel or taking a longer path is justified when learning more is the intention, which is kind of in the case for iGEM. So, despite everything, I do not entirely regret our decision to work with D. hansenii or to isolate a halophilic yeast from seawater.

A plasmid? Nah!

A fundamental task for most genetic engineering projects is to get a piece of genetic material into a microbe, a process known as transformation. When we attempted to accomplish that, our cells declined that alien genetic matter.

This is not uncommon in molecular biology. On iGEM Memes, an Instagram account from the Stockholm iGEM team, the issue was the topic of multiple memes, all pulling huge engagement from the other teams.

Having confronted this issue, we had to troubleshoot, eliminate the potential causes until we were left with the answer. Ideally, we would try adjusting one factor at a time, and observe whether the problem is fixed. But we were in no ideal setting, and with the limited time and not-so-scientific strategy we followed, the possibilities seemed infinite.

In a failed transformation, numerous suspects are to blame: the microbes, the media, the antibiotics, the plasmid, etc. Just one of them is enough to turn your head around.

Our failure to take a systematic plan in troubleshooting was mainly driven by our enthusiasm and the weight of the forthcoming deadlines; we tried modifying several factors at once. This was unquestionably not a smart tactic. It made the mission even harder and forced us later to take some costly shortcuts, like purchasing a kit for making competent cells (instead of preparing the cells in-house) just to spare us precious time we could've spent fine-tuning our competent cells protocol. There is nothing wrong with using a transformation kit, but we were forced to buy it, something we were not intending to and had to pay from our own pockets.

All of our accomplishments in the wet lab and the competition were made possible by our enthusiasm and passion, but that very same enthusiasm-driven mentality did indeed hold us back. It was not the most sensible strategy.

Documentation

Our first fundraising meeting went entirely undocumented, unless the shaky and low-quality photos are counted. This is just the tip of the stuff-that-went-undocumented iceberg!

Our outreach efforts were immense. We were hosted on multiple TV and radio channels, newspapers, and news websites. Our social media presence was noticeable. We held sessions for school students, university undergrads, and the general public. We even made a game to explain the concepts of Synthetic Biology. The documentation we did, however, did not do our efforts justice. It was brought to our attention by almost every member of the judging panel in their feedback.

Our journey to the US was not adequately documented; we do not have a recording of our presentation other than the live stream we shared on Facebook.

But documentation is not just about pictures and videos, a mistake resulted in no characterization of one biological part we constructed and added to the iGEM registry. We did not have a detailed-enough record of our first days in the lab; this was a side effect of our enthusiasm to get stuff done as I discussed earlier.

We were not oblivious to the vital role of good documentation. It’s just that we failed to execute this knowledge in a satisfying manner.

Master Procrastinators

On the eve of our presentation, we started preparing it … from scratch! It was after we finished the poster (also from scratch). Of course, we had a break after the effort we spent putting the final touches and looking for a place to print it.

Late in the night we terribly needed to sleep and became unfunctional, so we requested an Uber to get us to our place, but it did not. I made a mistake, putting Hynes Convention Center as our destination instead of the actual address. This rubbed more salts into the wound, resulting in us sleeping for less than four hours.

Procrastinating stuff to the last minute forced us to sleep anywhere. To the left is a picture that was captured 10 hours before the presentation, when we were not supposed to be there.

On the following morning, the slides were still half-done. I had to write (write not rehearse) my part in the presentation on the way to the Jamboree, 3 hours before it would be our turn to take the stage.

We managed to pull it through. The presentation was not as great as we dreamed of, which is fine, but it was not as good as we are capable of, and that is a failure. Part of this was out of our hands, half of the team had to leave for serving mandatory conscription, and were only allowed to leave and travel to Boston days before the Jamboree.

It's normal to sprint in the last mile, but what is not ordinary is to be on procrastination autopilot. Maybe our failure was a prioritizing problem? What I'm sure about is that we should have done it differently.

Else?

That was not everything. In our fundraising efforts, sometimes we underestimated ourselves, asking for only a small amount of money when we clearly could get more. My mobile rang while we were live in a radio interview, despite the host specifically asking us to turn it off multiple times before the interview.

On occasions, we failed to delegate tasks efficiently. The wet lab note-taking was a disaster, and trying to improve it by using Electronic Lab Notebooks (ELN) made it worse until we eventually reached a working formula.

Before establishing our team Facebook Page, we started another one named after the synthetic element Einsteinium, trying to raise awareness about Synthetic Biology. It was a mistake not to start with an official page for the team. And finally, our university did not participate in the iGEM 2020 competition, which was one of our top goals!

Failure is a fundamental part of scientific research. The iGEM competition is no stranger to that, and adds to it by being a student-led competition, with limited time and usually scarce resources.

Our mistakes, failures, and blunders taught us invaluable lessons. The barriers we had to overcome (or on some occurrences, live with), such as the lack of funding, the delays in shipping due to customs and regulatory processing, the lack of some critical equipment in the lab, losing half of the team members in a crucial time, all contributed to the outcome we ended with. But it was, just like our mistakes, a part of the journey, and the journey proved to be as crucial as is the destination. I wrote an article on why it's awesome to participate in iGEM competition, and I still stand by every word written there.

Today, more than a year after posing for our bronze-medal-winning announcement, reflecting on the journey that led us there, with all of the obstacles, the lessons, the achievements, and the falls, I could not be more proud!

This guest blog post was originally published on Youssef’s LinkedIn on November 6, 2020. Check out Youssef’s LinkedIn page for more of his articles and thoughts on iGEM.

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