Cloaking myth with math

In light of my last post, I thought I’d bring up that while those people’s bashing of Caitlin was ill founded, they are expressing an underlying problem that exists in any endeavor based on technology or science.

Too often, people use technical mumbo jumbo to cover a basic lie.

Beta cells burst

When my mom was alive, one of her studies was beta cells. These are the cells in the pancreas that secrete insulin. They’re actually, normally quite boring, except for a coincidence of two things in the 90’s.

The first was that people started creating organic compounds with long conjugated chain that would bind to various things.

To understand the importance of this consider the problem of DNA sequencing. This has always been done using chain terminated sequencing as described in the link above. What this means is that get some DNA, make a huge number of copies, and then lop off the copies at various points and replace the end with a radioactive compound which binds to the different bases. You then let the DNA migrate down a gel, and it’s migration speed will vary according to how big it is. You stop the migration, drop a piece of film over it, to let the radioactive compound expose it. And violá, you can read off the DNA sequence.

The problem with this whole process is the radioactive compound. As I used to joke with a friend in college, “that problem means you need to hire a graduate student instead of a machine.”

A clever solution was to stick an organic compound with a long conjugated chain instead of a dye. Now a nice “intro to organic chemistry” property of conjugated chains is that they vibrate and emit light when excited. This means you that when you shine UV light on it, it will reflect visible light. You vary the length of the carbon chain depending on which base it binds to so that each base at the termination emits a different color light and you simply watch the colors go by. There is a small complexity here because the different length of the chain changes the molecular weight and thus the migration speed, but you get the idea: no more graduate student!

Now apply this same technique to calcium ions. You can actually see the calcium concentrations fluctuate across the beta cell. And they did and something interesting occurred.

In some cells, not all—let’s say mouse beta cells, but not human beta cells—you got “bursting” where the calcium fluctuation would burst across the cell. You could see it with your own eyes under a magnifying glass. Pretty neat, huh?

The problem was the computer models at the time did not predict bursting at all.

Science is really messy

Fixing the beta cell model was no problem for my mother. The problem was her paper got rejected. I remember her showing me the rejection letter in the 80’s to ask me if I could identify what computer the reviewer’s comments was written with, and could it have possibly been the same person who wrote this other thing? My answer was the affirmative, implying that the reviewer was a scientist who had stolen her work previously.

She submitted her paper to a lesser known journal and got published.

And then “neuroscience” came

The 90’s marked the “decade of the brain” which in “messy science” terms meant that if you could relate your work to nascent field of “computation and neural science” you were more likely to get grant money than not. Oh there were other consequences, like the mind-body problem became a hot topic again in philosophy…

In any case, the beta cell became “hot” again because of it. It made a simple and perfect “single cell model” for a neuron: calcium comes in, some weird shit happens electrically on the surface of the cell, insulin comes out. Cool.

So it happened that this was the time the person who stole my mom’s work was presenting his paper on having “discovered” a model that correctly simulated beta cell bursting, to a marginally packed audience at a biophysics conference somewhere.

My mom was in attendance.

The presentation consisted of two parts, the first was an experiment he had done on human cells that showed the by-that-time much-observed beta cell bursting. In the second part he whipped out his model (actually my mom’s model), performed the same experiment on the computer, and showed how the computer model simulated the same results.

At the end, my mom didn’t wait to be called on. She stood up and said, “I like to say a couple words. The first is I published this model last year, and the second is that his cells don’t burst.”

The reaction in the crowd was silence followed by a few of the people suddenly doing a “heads on forehead” surprise.

“His cells don’t burst”

My mom wasn’t the easiest person to understand, but I assume you gathered the first part from my discussion: that she was expressing personally to the other guy, “this time you weren’t able to steal my work because I managed to get it published somewhere.”

The second part, the part that caused the surprise among a few in attendance, is far more fun. It might help to explain that those few were experimentalists who researched the pancreatic beta cell specifically. There is no way experimentally that the beta cells he performed his research on could burst; it was of the category that do not exhibit that behavior.

Until my mom mentioned that essential, but important detail, the fact had slipped passed the minds of many of the people whose job it was to notice such things: his (experimental) cells, do not, cannot burst—the “experiment” was a fabrication.

I asked my mom, how come they hadn’t noticed this earlier. My mom said it was because of the computer model. “Biologists,” my mom shrugged, “they see a slide with math on it and their eyes open wide and their brain shuts off.”

Opening our eyes, not shutting off our brain

So when you read my blog, or any blog purporting to talk about something technical, I hope you don’t be guilty of this error. I make a lot of mistakes, and I hope most of them are innocent and I invite you to correct them.

I also hope you don’t use math or technical discussions as a bludgeon to beat your opponents into submission. I know I’ve been guilty of that too, from time to time. I hope that I can acknowledge the essential truths of some of the things people say without destroying them on a technicality. If I keep doing this, eventually you will “shut your eyes” to me and I hope that doesn’t happen.

By this same token, let us be careful to not shut off our brain in the process. If we can think critically, we can add to the discussion.

An example for today

Here is one sent to me today. In the article, which compares various HD cameras, they write about the Sony HDR-FX1: “It also isn’t capable of as high of resolution as the HVX or the XL H1.”

Wonder why I am quick to bash Canon zealots sometimes? Read that again and realize that the Canon XL-H1 has the same Sony-manufactured 3CCD sensor as the Sony HDR-FX1.

(BTW, the Pansonic AG-HVX200, while capable of better quality in some instances, doesn’t have more resolution than the Sony HDR-FX1 either. In most cases, the resolution is worse. I explained the gory details of that in this article.)

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light writing, word loving, ❤ coding

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