Aizan reads stuff #5

Saturday May 4, 2019

‘Deep medicine’ will help everyone by Yoni Maisel on STAT. This is about a person with a very rare genetic disease called the common variable immune deficiency (CVID), a disease that affects the (adaptive) immune response, leads to failing to build seroprotection (a.k.a producing antibodies). I was impressed reading this account knowing that this person spend nights & days sifting through medical literature and eventually found out the genetic root cause, and he asked doctor to order the tests that he learned from his reading. He had to pay for white papers because some of them were behind paywall, which is quite sad.

“Please draw my blood and send it for a total immunoglobulin count. And please test me for antibody titers; I recommend pneumococcal and tetanus.”

This article is a nod to Eric Topol’s book, Deep Medicine.

Scientists Need to Talk More About Failure by Emily Dreyfuss on Wired. This caught my attention:

When it is, scientists go back, observe more, get new measurements, come up with a new hypothesis, and test again. And again.

It is hard to talk about failures out in the open. Science is an endeavour that requires a lot of effort but in turn the yield is kind of low.

Router vs Switch vs Hub vs Modem vs Access Point vs Gateway by Aseem Kishore on Help Desk Geek. I was confused about hub, router, and switch. The question that I had was whether (ethernet) switch also assigns IP (i.e. can act as a DHCP server). Answer: no, a switch does not give out IP address. That is what a router does.

A somewhat longer explanation: switches operate on Layer 2 (data link; moving frames), whereas routers work on Layer 3 (Network, moving packets and routing) of the OSI model. We deal with IP addresses on Layer 3. As for switches, they mostly deal with MAC addresses for moving frames from one to another connected device.

Computer networking is quite fun to learn. I wish I know more about this because sooner or later I would like to deploy my own homelab server farm.

The Antibiotics Business Is Broken—But There’s a Fix by Maryn McKenna (!!) on Wired. The story begins about a failed biotech company, Achaogen, a startup that were trying to bring to market an antibiotic drug, plazomicin (it got FDA’s approval, btw). Then, the story continues talking about the problem with marketing antibiotics drug: only being consumed for short period of time (lest resistance appears) and short window before, well, resistance happens regardless what you do to prevent it from happening.

Then, the real meat of the story talked about the failed “push” incentives to bring antibiotic drugs to the market, because often times (big) grants are dispensed early on before/during the R&D phase. The alternative, the “pull” incentive, works the other way around: rewarding those who did well with R&D, and pull them to get into the market.

So, the push alternative is like “here is a good amount of money, do all these from basic research to clinical trials”, where pull alternative is like “you better be damn sure your drug works out well, then we give you money to get into clinical trials”.

The entrepreneur behind the cancer immunotherapy revolution by Matthew Herper on STAT. This is another good long-read, talking about the story behind Keytruda, Opdivo, and Yervoy (the immunotherapy drugs). Like every other successful science story, the success of immunotherapy was not built on just 1 person, rather a number of people with different perspectives. In this context, Nils Lonberg and Alan Korman, who helped bring the drug into the market.

By the way, Lonberg worked together with George Church (yes, that George Church) and they were students in Walter Gilbert’s lab. Yes, that Gilbert, as in Maxam-Gilbert sequencing.

Fun story by the way.

How a Wi-Fi Pineapple Can Steal Your Data. A friend brought this to my attention after I posted a picture of a wireless travel router on Instagram Stories. So, what is this about? Essentially, here is a device with a price tag of $99, capable of doing MITM-type attack, it has its own web interface to make pentensting life easier. Reading this makes a stronger case that browsing public WiFi must be done through a VPN. I recommend Wireguard, if you are more on the technical side of things.

The Principle of Charity: On the Importance of Using Constructive Arguments. I saw this on Hacker News and it came to me that this is something important. There is a this reply on the Hacker News that read like this:

Before you can say “I disagree,” you must be able to say “I understand.” It is axiomatic that before you level criticism you should be able to state an author’s position in terms that he or she would find acceptable. After that, you may proceed in any of 6 directions.

But importantly, this assumes that the assumption of good faith is well founded between two people that are disagreeing. Hence, this Principle of Charity has a somewhat strict criteria to it, that both of you are engaging in a good faith. After all, the Principle of Charity states that:

It is the idea that when criticizing someone’s argument, you should criticize the best possible interpretation of that argument.

Read this article. It is good. However, Principle of Charity can be done when it is reasonable to do so. Life is too short too argue with anyone everyone. Internet is a toxic place to begin with nowadays. As mentioned in this argument, the Principle of Charity utilizes some form of Steel Man Argument (as opposed to the Straw Man Argument), in that you reinforce the view that opposes your value before you disagree/attack it.

How I draw figures for my mathematical lecture notes using Inkscape. This is a real definition of a mad lad. Previously, Gilles Castel wrote how he uses LaTeX and Vim to take notes in mathematics lectures. I was already impressed with the write-up. And now, he came back with another write-up on how he uses Inkscape in such a way that was unthinkable to me before: lots of custom key chords for rapid shape styling. He turns his Inkscape setup into something that feels kind of similar to using Vim, except for drawing stuff.

The way he uses Vim, LaTeX, and Inkscape is and mind-bending. I hope he continues writing more and more in the future. He is my kind people since his primary workstation is linux-based.

Unraveling the JPEG by Parametric Press. Here is one interesting bit that I learned from this article:

Rods, the other type of receptor we have in our eyes, can only detect changes in brightness, but they’re far more sensitive. We have about one hundred and twenty million rods in our eyes, compared to a measly six million cones. This means our eyes are much better at detecting changes in brightness than they are at detecting changes in color.

Which, sort of explains as to why flow cytometry can be used to quantify population sample with more than 12 colors and why we are mostly limited to 3-4 colors with microscopy, be it confocal, multiphoton, or super-resolution.

In this article, chrominance refers to color, luminance refers to brightness.

An Introduction to Streams by Lucas F. Costa. The single biggest contribution from this article is the definition of file descriptors. By default, the file descriptors 0, 1, and 2 correspond to stdin, stdout, and stderr. Long ago I remember writing startup script like this:

command runsomethinghere.sh 2>&1

This means “hey this script, just dump the error from stderr into the same file descriptor for the stdout.

Transfer of antibodies in breast milk of humans on Biology Stack Exchange. This has been on my bookmark for a very long, long time. So I thought about getting rid of this once and for all. The accepted answer links to a review on PubMed, Perspectives on Immunoglobulins in Colostrum and Milk. Here are some interesting things:

Mother transfers secretory IgA (sIgA) to protect the mucosal surface of the infant (trachea, gut, etc). However, sIgA is not completely resistant to the proteolytic degradation, hence the reason why the infant should continue on breastfeeding for a certain period of time. On the other hand, IgG transfer happens when the baby still inside the mother’s womb, to which the transfer happens through the placenta. Hence, the baby would have protective antibody circulating in the blood and also on the mucosal surface.