This week we heard each other’s presentations for the various CRISPR applications and I was most interested in the one presented by Sophia, whereby the paper investigated the use of hairpin secondary structures to improve accuracy. I feel like there would be a lot of potential if they are able to show more accurate evidence of its effectiveness because forming the hairpin structure itself appears quite simple and straightforward. However, being based on mathematical modelling, I had a tinge of doubt towards the accuracy of the results, more so when there were no previous studies or reasons sited for choosing their modelling software used. From this it made me question how easy it is for us to take for granted certain methodology, especially when it is either well-established or commonly used.
Personally, I thought it would be easier to analyse a short paper, but I was proven wrong. My own paper was theoretical in nature so, in terms of methodology and materials, I really struggled to find points to critique. But at the same time, the short article made me appreciate every line that was written, after having combed through each line over and over again. While critiquing the paper, I kept wondering, “Why didn’t they include this (or that)?”, and that is when I realised how important it is to accurately communicate information in a succinct manner. There are certain things that seem important but may not be relevant to the current proposition. The author has to re-evaluate the direction and focus of the paper and ascertain if the content is in line with the message to be conveyed.
I always look forward to our field trips, so I would say that the highlight for this week would be the trip to NovogeneAIT. Before the trip, I had been to Biopolis before and I knew it to be a hub for government agencies and other government-supported research companies. From what Robson had shared during the tutorial, I had the impression that NovogeneAIT was a very big company (given that they had multiple sequencing centres around the world. I’m not sure if I was mistaken but I think he was referring to the sequencing centres of Novogene, right? NovogeneAIT being the joint venture only here in Singapore. In any case, this made me expect a much larger space, so I was very surprised when they gave us a tour of a much smaller area. Nevertheless, I think that this still impresses me because they are able to process a large number of genome samples even with this small space and equipment. It really speaks for how advanced the processing of the HiSeq and NextSeq they are using is, that these few machines alone can produce so many libraries.
On that note, it really interested me when they were talking about the eventual goal to be able to sequence a full human genome for just $100. In a matter of a few years, the price has gone down to just around a thousand dollars compared to how expensive it was before. That means that one day, sequencing will become so readily accessible at an affordable price, we might be able to advance research at an exponentially fast rate as well since genome sequencing is being applied in many scientific areas. On the other hand, it also implies the business race of manufacturing companies to design faster and more advanced processors to be able to handle even more data at a cheaper cost. Seeing the sequencing machines reminded me of the development of computers from really huge machines that take up an entire room to the laptops and iPads that we see today. I look forward to the day we will be able to have a table-top sequencer that can process as many samples as the latest model of NovaSeq today.
One of the confusing things for me was the fact that they still relied on physical servers, although they are looking at exploring cloud servers and cloud processing. One of the biggest limitations is that they have to clear the servers of old data after 45 days, and only the processed data is being backed up into their cloud server. What if a client wanted to retrieve old data that was past 45 days? Or what if they wanted the raw data for some reason? Data storage is a big issue for a company like NovogeneAIT that has to handle terabytes of data every day. I think that data management is really important not just for big companies but even on an individual level. Keeping things organised and backed up properly makes it easier if you need to pass on the data to someone else.
This week we had a more in-depth look at the CRISPR-Cas system for the lecture. I think that it is very exciting when you realise that we are still at the tip of the iceberg when it comes to understanding the role and functions of Cas proteins in bacteria. And yet we have already discovered Cas proteins that are able to not just produce a double-stranded break but produce a single-stranded nick and even sticky ends. Repeatedly, however, seems to be that the real bottleneck of this technology is managing the offsite targeting effects. This still leaves room for error and with regards to clinical therapeutics, this is definitely something that you would want to eliminate as much as possible. We are however in a time when CRISPR-Cas system gene therapy is likely to see way more applications, as scientists continue to understand the functions and possibly uncover more immunological defence systems in bacteria that may help us too. The assigned readings (and their diagrams) really helped me to understand the mechanism of the different Cas proteins because initially, it was difficult to conceptualise. And the lecture helped to consolidate my understanding by reiterating what I had read beforehand.
I must add that the guest tutorial by Novogene AIT was a good addition to the week as it fed my interest in the business aspect of biotechnology. It must be quite hard to “stay ahead of the competition” all the time and is probably not as simple as the speaker had made it be. Understandably there are probably some marketing strategies he is unable to reveal, even though I wanted to know how exactly do they have intel about the latest software, technology etc. Trend analysis is also something that interests me, so I was glad to hear about how they work towards trying to predict the needs of their clients beyond what they request from them, showing them that the company is able to provide more services (and at the same time making more profit!). The idea of master contracts is also pretty strategic, instead of just targeting individual labs. With Singapore being very small, however, I can see why geographic segregation is also necessary. This idea of a concerted effort really pays off, not just in business but in everyday life. It is not efficient to divide your energy in too many places. As a service provider company, working closely with government agencies/authorities is probably a good move too. In Singapore where the government nowadays concentrates its resources on a lot of data-driven projects, such contracts provide a lot of stability and reputability. Lastly, the speaker’s comment on being a service provider in today’s economy really struck out to me. Being someone who is currently thinking about having my own business one day, it was really relevant advice. With today’s sharing economy, being a service provider is very advantageous and this business model has a lot of potential given the right service in demand!
Yesterday morning, as I was eating in the dining hall, someone came up to me and said hi. Here’s how that conversation went:
F: “Hey Jan, how are you? I saw from over there and saw you with your eyes closed for so long.”
J: “Oh, I was praying.” I smiled.
F: “What, oh sorry. Usually people pray really fast. Is there so much to be thankful for anyways?”
J:”…there’s always many things to be thankful for, especially for surviving this hectic week.”
H: “Yea, she always prays very long (before meals), and that’s a good thing.”
I’m really fortunate to be living in a time and place where I’m able to openly practice my faith. People in my RC, for the most part, are very understanding towards their Christian friends who say grace before meals. I guess the more you are around people of different race and religions you tend to become more empathetic when you understand their practices.
At the same time, I’m very fortunate to have meals with friends who say grace too, because I feel that our prayers together are so much more beautiful.
So whether or not you practice praying regularly, I just wanted to remind y’all that if you take time to reflect, there’s definitely a lot of things to be thankful for.
And there’s no need to rush through saying grace, you realise you’ll enjoy your meal a lot better.
Sunday marked the end of Project KaHU and it felt truly bittersweet. I was so relieved to have completed this 5 month journey of ups and downs. The final sprint was complete. And at the same time I know that I will really miss this batch of mentees and I can’t imagine how much we have impacted them, but I’d like to think that we made a difference even in the slightest.
This experience was a first for me. At the start, I was so overwhelmed and I kept telling myself, “This was not what I signed up for.” But I’m glad that I got to work with this KaHU team and I couldn’t have done it any other way. They pushed me to explore things I’d never imagined I’d do. And if you told me that I’d be in pulau ubin again, I’d never believe you. I’m happy and fulfilled with what we have achieved together.
Project KaHU 2018, signing out.