Reframing the Gluten Scanner

A lesson that every scientist (or any person in a fast-paced creative field) learns: be glad when we find out that our research idea has already been done.The situation can be re-framed as follows:

  1. It’s awesome that there are others working just as hard as you to better the world.
  2. Reassurance that you’re not idiotic.
  3. You can now devote your precious time to developing your other projects.
I learned this lesson in 2011. After proving myself competent by assisting others in the robotics lab, I was encouraged to pursue an independent research project.
I excitedly came up with a list of ideas, then progressively descended into disappointment.
In the crowded lab, I said aloud, “It seems that every project I come up with has either already been proposed or wouldn’t be funded”.
To which the senior engineer in the lab (whom had not spoken to me before) responded, “Welcome to science!”.

One of the main projects that I’ve been working on is a gluten scanner.

The scanner allows those with food allergies to avoid accidentally poisoning themselves. This is done in one of two ways:

Raman Spectroscopy Method

  • Identify the minima and maxima on the absorption spectrum of a given protein (currently gluten) with a 1D array of IR / Vis lasers and an Avalanche photodiode Si(c).
  • Perform differential data analysis to determine if the food is contaminated.

This scanner would be able to analyse the food ~>1cm in depth without effecting the food, whereas (if desired) taking a small sample out of the food at an opportune sampling point allows for deeper results.

Originally planning on taking spectroscopic approach, I found that it was incredibly noisy (see below) to detect gluten in a vinegar solution [gluten is insoluble in water], let alone amongst protein rich food!

Thank you, Sunnyvale Biocurious, for training Paul on the spectrophotometer!

Realizing the specificity of the antigen-binding sites on antibodies, I came up with the following biomarker approach to significantly increase the accuracy of my device.

Biomarker Method

Gluten is a protein composite of gliadin and glutenin (stuck together with a starch). G12 and A1 are antibodies that bind to gliadin (a highly immunotoxic 33-mer peptide).

Although A1 has a higher sensitivity to gluten (0.33ppm) than G12 (0.5ppm), most Celiac patients have a 20ppm poisoning threshold (far below both thresholds). G12 is far less expensive, and thus the better option for regular consumer use if you aren’t willing to synthesize your own antibodies in bulk.

Anti-gliadin antibodies can be paired with a colorimetric assay to form a biomarker-based detector in the form of: a toothpick-sized detector to poke into food || the gluten-detecting equivalent of litmus strips.

G12       (Image credit: PDB)

In the past few days, I found that there are a set of devices, GlutenTox, which use my planned approach. Since this realization, I’ve also come across 6sensorlabs, and the TellSpec.

It seems to me that these solutions are not cost-effective enough to be sustainable for daily use. This is likely because antibodies are expensive unless you bulk synthesize them.

Finding Routine in Freedom

I’ve just recently taken on a contract project. Adding that project onto my wheelchair and protein detector projects is a fun exercise in multi-threading that contributed to a recent realization.

After graduating and moving out to the Bay Area, I found myself missing the soft structure imposed by university. Two week ago, I finally developed an improved soft structure (independent from academia) to govern my time-expenditure.

It’s exciting to find a routine that works for me in an environment with many more degrees of freedom than I am accustomed to!
The schedule I’ve found is approximately:
08-09 Wake (Coffee)
09-10 Stretch, read papers, and sort todos 
10-11 Check email
11-12 Ab workout/Jog
12-18 Research
18-20 Climb/Bike
20-22 Blog/Research/Draw
22-24 Socialize and reflect on day (lessons learned, significant events and time allotment)

The lovely thing about this schedule is that I have no issue adjusting the time frames to suit my priorities that day. Life is a dynamic environment, but I’ve found most of my days fall into (at least) a permutation of this pattern. Having this structure to reflect on and shape my choices has noticeably increased my productivity and focus.

I hope you have a similar flexible schedule! It is a beautiful feeling to find routine in freedom.

The Utility of Art vs. STEM

I was recently asked an interesting question in an interview:

You stated in a previous article that you believe math and science are “toolkits” to solving problems in ways that writing and the arts cannot. Can you elaborate on that? 

I think science and art are two sides of the same coin. The distinction is quite fuzzy for the fields overlap in a variety of ways that depend on the perception of the viewer.  For example, mathematicians find aesthetic beauty in eloquent proofs and concise equations. The main difference between the terms lies in what they contribute to the to the world.

Art provides inspiration and science provides understanding and explicit utility. I specify “explicit utility” for implicitly, inspiration provides the driving force for scientific advancement.

Art enables us to describe every emotion and experience known to man, but mathematics enables us to understand the laws that govern everything. Art cannot show us something that is not a human experience, for it is limited by the person who uses it. Mathematics, on the other hand, can show as absolute truth realities too grand to be fully understood by the human mind while science allows us to precisely and repeatedly implement these truths in the physical world.

Betrand Russell::> Mathematics, rightly viewed, possesses not only truth, but supreme beauty — a beauty cold and austere, like that of sculpture, without appeal to any part of our weaker nature, without the gorgeous trappings of painting or music, yet sublimely pure, and capable of a stern perfection such as only the greatest art can show. The true spirit of delight, the exaltation, the sense of being more than Man, which is the touchstone of the highest excellence, is to be found in mathematics as surely as poetry. 

Controlling Fear

Having a reliable method to control your fear and achieve focus quickly is indispensable.  During one sleepless night reading Frank Herbert, I discovered my solution.

A bit of backstory:
During undergrad, it was common before and during tests for me to be unecessarily nervous. This degenerated my ability to focus and fully apply myself to the important task at hand: aceing the test creatively in a reasonable time frame. 

While meditating, one of my many calming methods is the recitation of poems, such as the Jabberwocky, Litany Against Fear, and If. I find that of all poems, the Litany calms me the most quickly.
To immediately calm myself in risky situations, I use the same techniques. My favoured methods are solving simple integrations or reciting the Litany Against Fear
This Litany, from the Original Dune, an “incantation spoken by many highly educated people who faced danger or fear during their everyday lives. The incantation helped focus their minds in times of peril.” 
The content of the Litany:
I must not fear.
Fear is the mind-killer.
Fear is the little-death that brings total obliteration.
I will face my fear.
I will permit it to pass over me and through me.
And when it has gone past I will turn the inner eye to see its path.
Where the fear has gone there will be nothing. 
Only I will remain.
If you aren’t sure how to begin searching for a reliable and personalized method: think of things that make you happy and calm and read while simultaneously reading the Litany aloud to yourself. 

18 General Lessons I Learned in University

Some of these may seem obvious; keeping their importance in mind is not so obvious.

Through my experience as an undergraduate, I’ve found that the following lessons are useful to be aware of. Hopefully, they will help you and those you love avoid unnecessary suffering. Some of these lessons overlap and they are not in order of priority.

I recently received the Thiel fellowship, and wrote a seperate post on additional lessons I’ve learned.

0. Putting as many hours as you can into doing what you love pays off.

The best programmers I know started programming as a hobby first.
The best researchers I know started researching as a hobby first.
The best mathematicians I know started playing with math as a hobby first.
The trend continues and transcends disciplines of study.

1. Don’t lie about your knowledge base.

It’s better to say “I don’t know.” People respect honesty and pure intellectual pursuit/curiosity more than your pride. Plus, you learn more that way!

2. Don’t cut corners.

Build up your knowledge base from understanding.
Put effort into doing (even tedious or arduous work) as well as you can. By doing this you may discover passions you wouldn’t expect!

3. Fix your procrastination habit.

Don’t know how to fix it? Read this.

4. You can do anything but you can’t do everything. 

Don’t start an entirely different project each day.
Good quality work is done by working through the tedium inevitable in the details of a complex project, and thinking of each step as a new project.

Sort out your priorities and keep them in mind.
Good food, exercise, and sleep are foundational to long-term functionality.

5. Create your own motivation.

Do things in chunks, reach the “mindset”, if you hit a wall, come back to it, you will ponder it unconsciously.

You have to assign your own meaning to life – no one will do it for you. The rules and meaning I live by are an improved version of Neil DeGrasse Tyson’s philosophy:

1. Stay healthy.
2. Learn [and make] something new every day.
3. Lessen the suffering of others.

Keep these in mind; these simple rules changed my life for the better.

6. Being a Jack of All Trades is itself a talent.

Limiting yourself to the current ideas of one discipline makes original research unnecessarily difficult. I find original research is really just connecting past ideas into a new idea that is more than the sum of its parts.

My friend Adam Munich wrote this lovely post detailing the dangers of overspecializing. I highly recommend it!

7. Be aware that friendly curiosity occasionally comes off as interrogation.  

I’ve recently begun briefing myself with: “I’m an incredibly curious person, feel free to stop me if I’m asking too many questions.”

8. Don’t fear failure.

Giving up before you begin is far worse than failing.
Don’t waste opportunities due to fear of failure and cling to the theoretical hope offered by the past possibility of success.

9. You can’t please everyone.

You will quickly exhaust yourself trying to conform to the needs of all.
If you are motivated, honest, kind, and aware of (and abide by most) social norms, fearing the opinions of others is largely unnecessary. Many things that work for others may not work for you and vice versa.
Don’t feel obligated to help everyone that requests your help.

10. Have a workspace.

Make yourself a workspace that you can retreat to and feel at home in.
I have some friends who prefer to work on different task types in different places, and others that enjoy using one workspace for most if not all of their work. Find your preference.

11. Accept compliments.

Compliments are mostly beneficial to those who give them.
“Thank you, that’s very kind of you to say” is my favored response, for it is truthful.

12. There is a difference between nice and kind. 

In my opinion, the difference lies in your motivation.
Being kind is honestly (and gently if possible) doing what is best for the other person.
Being nice is saying what they want to hear.

13. Communicating your ideas is an important skill.

Keeping the audience interested during public speaking is is of equal if not more importance to the content of your speech.

14. Credit your collaborators and prior art.

Don’t claim the work of others as your own.
Keep a log of your contributions to a project to avoid IP disputes.

This applies to homework as well: Making use of the internet to research a problem is to be encouraged as there could be hidden treasures of mathematics to be discovered beneath the surface of many of these problems. However, there is a fine line between researching ideas and using the answer you found on another website. If you photocopy a crossword solution then what have you achieved?

15. Stuck? Explain it to someone.

If you are stuck on a problem, explain the problem, then brainstorm or bounce your ideas off of a friend.
Can’t find a friend who will listen? Explain it to yourself out loud or free write.

16. Write it down.

Although possible to keep all of your project plans and todos in mind, a purely mental method is an unnecessary burden. Writing things down significantly lowers my stress level.

17. If you don’t immediately find your passion, fear not.

I switched my major from:

$\rightarrow$ Psychology/Studio Art
$\rightarrow$ Anthropology/Studio Art
$\rightarrow$ Math
$\rightarrow$ Math/Computer Science
$\rightarrow$ Math/Physics
$\rightarrow$ Electrical Engineering
$\rightarrow$ Computational Physics.

Playing in these disciplines I’ve discovered that what makes me happy is implementing my passion for STEM to enable the disabled. I wonder what you will discover!