3D barcodes: The Heuristics of Calculus and the Unrelated Density of Information In Cell Biology.

[NNadir]

Last edited Sat Jan 20, 2018, 03:44 PM - Edit history (1)

Abandoned by his alcoholic father, my father dropped out of school in the 8th grade to go to work - he shined shoes for a living until he joined the Navy in order to be sunk by the Germans, and shot at by the Japanese. He never went back to school, using his GI benefits not for an education - since it would have involved time to get a GED, and then go to college - but to buy the house in which I grew up.

His main interest in mathematics was to ask me to calculate the area of things when he worked in the woodshop he assembled in the basement, where he worked whenever he wasn't working 14 hour days packed with overtime so he could afford to buy me and my brother trinkets.

I was never able to teach him the 9th grade math required to calculate areas beyond squares and rectangles for himself, but he made stuff anyway and I helped him whenever he needed it.

All this said, the most important thing about buying a house for my father was the schools, and looking back for its time, I was educated in a pretty good school district, at least for its time. My house was a lower middle class neighborhood in an otherwise upper class professional school district. Before the age of the minicomputer it was one of the first schools to have any kind of computer - you put the hand receiver into a special holder to contact a main frame somewhere at some national lab - and one of the few schools around where students could take a calculus course before going to college.

These things are of course ordinary now: My son took three courses in calculus in high school, repeating the third one in his first year at his university to be sure that nothing was missing, only to report that taking the class was largely a waste of time except as a review. Like most children, too, he grew up using computers far more powerful than those used by the best engineers of my childhood and teen years, the NASA engineers who built the American space program that led to all the discoveries that now define our ordinary lives.

Nevertheless, looking back on my high school calculus education - where I was a "good" student, in the top ten percent in a school where everybody else's father was an engineer, a physician, a pilot, a Park Avenue lawyer or some such thing, although my father drove a forklift in a unionized warehouse - I realize that my mathematics education was extremely deficient in important ways.

Looking back, I realize I emerged with some very profound areas of ignorance, the most important being the belief - which no one corrected - that mathematics was just an abstraction, a cute curiosity of little practical import, except of course, to calculate the area of a table top so you knew how much wood to buy.

Seriously. And that was a "good" school.

I think it's a serious disadvantage - one that our culture should do everything to address and overcome, even our government is notable for its profound contempt for and hatred of poor people, unlike the Jesus they always prattle on about - for a child to grow up with uneducated, or poorly educated parents. (Look how stupid Donald Trump Jr. is, for example.) We waste time and resources, critical human resources, when we fail to value our teachers and fail to understand what they need to be trained to understand about the minds of children, and the stumbling blocks those children face.

When my boys were growing up, I made sure to discuss with them the concept of what a dimension is - I thought while growing up that a "dimension" was a fuzzy topic in some science fiction books where travelers from "other dimensions" traveled to our world - which is to say that a dimension is best regarded as a scalar value comprising a vector. One of the things my sons understood before going to high school was that three dimensional space as represented by the x, y, z co-ordinates is just an arbitrary way of translating other systems having multiple dimensions into easily visualized geometrical structures. My oldest son, the art student, confers with his brother, the engineering student about vectors while figuring out how to program web pages. It's ordinary for them, but it was in no way ordinary to me, even after I went to college.

This why it was such a pleasure for me to come across this very nice paper on cellular biology: Three-Dimensional Barcodes with Ultrahigh Encoding Capacities: A Flexible, Accurate, and Reproducible Encoding Strategy for Suspension Arrays (Si Lu, Ding Shengzi Zhang, Dan Wei, Ye Lin, Shunjia Zhang, Hao He, Xunbin Wei , Hongchen Gu, and Hong Xu, Chem. Mater., 2017, 29 (24), pp 10398–10408).

The authors - from Shanghai Jiao Tong University Affiliated Sixth Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University - wrote in the abstract, for the reasons above, strike me, as a result of my upbringing, a beautiful statement to which I wish I'd been exposed when I was a child, to wit, this:

Novel 3D barcodes with an extraordinarily high encoding capacity are developed through a flexible, accurate, and reproducible method. Here, the three dimensions refer to the size, fluorescence emission wavelength, and intensity of the barcodes.

There you have it, three dimensions that are not really space related, with the possible exception of "size" which, in this case can be expressed as simple unidimensional scalar, the radius, since the particles are spheres.

Here is a picture, from the text of the paper, of the particles:



The caption of the picture is this:

Figure 3. (a) SEM image of the QHPs (red signals are pseudocolor). Histogram plot for the q0–q7 S-QHPs (b) and Q0–Q9 L-QHPs (c) host codes distinguished by fluorescence intensity via flow cytometry. (d) SEM image of the DMBs showing the host–guest structure (green and red signals are pseudocolor). Histogram plots for f1–f5 (e) and F0–F5 (f) guest codes distinguished by fluorescence intensity via flow cytometry. Confocal images of the q6f5 S-DMBs (g) and Q6F4 L-DMBs (h) recorded at different focalized planes from the top to the center of the cross section through different channels. Images in the first and the second row were observed at channel 2 (from 595 to 625 nm) and channel 1 (from 500 to 530 nm), respectively; third row is the merged image of the first and second row.

The purpose of these highly dense information systems is described in the text of the paper:

As the field of systematic biology has progressed, the need for multiplex assays involving the simultaneous detection of multiple targets in a single sample is increasingly developing.(1, 2) Suspension arrays, benefiting from fast binding kinetics, flexible array preparation, and multiplexed analytical capability,(3) are the most promising methods to meet this need. Barcodes, as the core elements of suspension arrays used to identify and capture multiple targets, should be enormously encoded and easily decoded.(4, 5) Compared with other encoding strategies,(2) such as chemical encoding(6) and graphical encoding,(7, 8) fluorescence-based optical encoding is the most universal strategy owing to its simple preparation, low cost, and well-developed decoding systems.(9, 10) Among the typical decoding systems used for optical barcodes,(2) flow cytometry has been most widely accepted because of its high sensitivity, accuracy, and fast detecting speed.(5, 11) From the perspective of time efficiency and sensitivity, the tandem use of fluorescence-based optical encoding and cytometry-based decoding is the mainstream barcode platform for high-throughput multiplex assays.

Nonetheless, in multiplex assays, the number of target molecules that can be assessed in parallel is restricted to the number of distinguishable barcodes in flow cytometry. To date, numerous successful cases have been developed to enlarge the encoding capacity of barcodes based on two commonly used encoding fluorophores, organic dyes(12-17) or quantum dots (QDs).(18-27) The most classical dye-encoding system is the commercialized xMAP technology,(15-17) where orange and red dyes are loaded in microscaled beads at 10 different concentrations by the swelling method. Hence, an encoding capacity of 100 barcodes has been obtained via flow cytometry.

Flow cytometry is a technique where individual cells - they could be cancer cells, or cells designed to be pluripotent cells to restore or regrow damaged tissue (or even, someday, whole organs), or cells for some other purpose - are isolated on an individual level so that one can learn something about them, it could be the biochemistry of their surfaces, or information about their genome, or something about their general chemistry of biophysics.

The authors write about building a coding system of particles:

In this study, we develop a novel 3D encoding strategy, as illustrated in Scheme 1. The 3D barcode consists of two types of isolated building blocks: a QD-encoded host particle (QHP) in variable microscales and a set of dye-doped guest nanoparticles with different fluorescent intensities. After assembling two building blocks together, a strawberry-like structure is formed, denoted as a host–guest structure. More importantly, there is no restriction to the type of fluorophore loaded in each building block as long as their fluorescence emission spectra have clear distinction. (sic)

Here's the schematic of "Scheme 1"



The caption:

Scheme 1. Schematic Showing the Three-Dimensional Encoding Strategy Used To Fabricate DMBs with Ultrahigh Encoding Capacities

"DMB" refers to "dual-encoded magnetic barcodes."

There's some cool chemistry and biochemistry in the paper, both analytical and biochemical, and the authors write finally in their conclusion thus:

In summary, we developed a 3D encoding strategy to fabricate high-performance barcodes with an extraordinarily high encoding capacity in a splendid accurate and reproducible manner. The three dimensions refer to size, emission wavelength, and fluorescence intensity of the barcodes, which could help enlarge the encoding capacity with ease. As a result, 100 distinguishable barcodes in flow cytometry were achieved controllably, firmly demonstrating the success of this encoding strategy. Meanwhile, the DMB-based five-plexed protein detection was also studied, and the satisfactory results verify the feasibility and effectiveness of DMBs in multiplex detection. Furthermore, the encoding capacity could be exponentially increased by utilizing MSs with other sizes, employing more types of fluorophores or importing other new encoding elements into the inner space of the host particles. Therefore, this 3D encoding strategy paves a new way to fabricate enormous barcodes, which exhibit immense potential in high-throughput multiplex assays.

A cool paper out of China where - say what you will about the Chinese government - the government doesn't hate science as much as the people controlling our government do.

I hope you have a very pleasant weekend.

[eppur_se_muova]

1. Your school was not at all unusual in emphasizing the practical over principle, unfortunately.

It wasn't until after my college years that I realized how much better-prepared for a scientific education I could have been. Many of my classmates came from the Northeast, especially the NYC area, and had received exposure to more advanced material at the high school level than I ever could have gotten in the South, despite being in a select group of math students who got an "enriched" curriculum, and despite living in the county with either the best or second-best school system in the state. I didn't realize at the time that, despite having always been an excellent student who was never forced to work hard at all to master the material, I was really at a disadvantage that I should have taken decisive action to correct.

Not to say that our teachers didn't try. It was just that I saw such a small portion of what real science, and real math, was like, that I never knew just how high it was possible to set my sights, and never worked all that hard to achieve the end goal -- it seemed like there wasn't that much more to learn, and it was all going to be easy. I've tried to catch up later in life, but of course it's so much easier to learn when you're younger, and especially when you have no other responsibilities to distract you from your own education.

For a great many professions -- or more accurately ways to earn a living -- such a rich education is not necessary. But our country really doesn't have any systematic way to find and nourish young talent in the sciences, particularly the abstract sciences, despite all the emphasis on "STEM" which politicians all claim to favor (at the expense of other subjects, but that's another story). If we could find and nourish potential scientists as effectively as we do potential professional athletes, think what a country we would have.

[NNadir]

2. Well, I grew up in the suburbs of New York City. I suspect my own ignorance may have...

...derived from the assumption on the part of the teachers in my school that "everybody knows that."

I didn't.

That is also dangerous, when one assumes that things are too obvious to teach.

One of the joys of growing old is to recall one's ignorance and to understand how one overcame it. (That, of course, is a joy that some people like the orange fool in the White House will never experience.) And of course, another joy is to realize that one will never stop being ignorant of many beautiful and wonderful things. Now that I am running out of time in my life, I am rushing toward all the things of which I am ignorant, and every day is more beautiful than the last, and all my days are beautiful now.

Even though my boys are far better educated than I was at their age, I hope they will experience that feeling when they are old men - if they become old men as surely I hope they will - the recollection of their former ignorance.

Their generation has many wonderful tools with which to work, but they also face challenges that dwarf those my generation faced, and that is because of my generation, and the way some of us, many of us, allowed ignorance to thrive in places where we should have fought it.

On a national level, I think we are seeing how the embrace of ignorance for ignorance's sake can cause great damage.

I hope we will be able to recover, for the sake of the young people. I sincerely want their world to as beautiful as mine was, for all the mistakes I made. It's not looking too good right now.