Fluorescence is amazing.  You can take a cheap dye, attach it to almost anything, and then detect that thing at absurdly low concentrations. Fluorescein is the dye in the picture above. I hit it with my blue LED illuminator, and it glows with an intense green light. I suspect that basically every glowing green sciencey thing in every movie ever was really just fluorescein. It’s also the dye that they used to use to turn the boston river green.  It’s also injected into human veins for an angiogram. Back in the day, I used a powerful laser confocal microscope to see individual fluorescein molecules.

Anyway, I love fluorescein. I’m going to use it today to talk about detection limits.

The other day I was talking about how “the dose makes the poison.” Some folks get all up in arms because of small amounts of (for example) formaldehyde. Chronic exposure to high levels of formaldehyde is bad. Acute exposure to gram-quantities could kill. But a single exposure to a microscopic quantity is not dangerous. It’s highly reactive and will be destroyed by formaldehyde dehydrogenase very rapidly.

When I talked about any level of formaldehyde being safe (it’s a metabolic byproduct! Your body knows how to deal!) I got accused of being a shill for “Big Pharma” (sigh). I tell you what: I wish it was that easy to get money from a pharmaceutical company. I say simple factual information, and they cut a check? Yes please!

I digress. The point is that just because we can’t detect it doesn’t mean it’s not there. And just because we can detect it doesn’t mean it’s dangerous. We get better at detecting things every year. That doesn’t mean the world is getting more hostile. We’re going to talk about quantifying the limits of our measurements today in my instrumental analysis class.

I put up a video honoring Friday the 13t superstitions. It has a movie of that fluroescein drop at the end and I’m pretty impressed with myself for how cool it looks.

I saw this Science News report on the analysis of how elephants are able to manipulate delicate things with their heavy trunks. At the end of it, the report talks about some justifications for why this information might be useful. For instance, a trunk-like robotic manipulator might be useful for search and rescue.

I think that might end up being useful, but I’m also just curious. How does the elephant do it? I want to know. The trick seems to be “virtual joints” that the elephant adjusts up or down the trunk length to support more or less of the trunk’s weight. That allows the trunk to be used for coarse or delicate tasks as necessary. That’s just clever.

I spend a lot of time trying to find a problem to solve. I think that the bio-detector particles that I am making in the lab will be useful for measuring biochemicals like cytokines. I think that measuring cytokines early and often will be useful for medicine. It turns out that there is significant diversity among humans in their baseline cytokine expression levels. So just knowing what is a normal, average expression level for one of these proteins is not good enough. To make sense of the data, we need individualized, normal, baseline measurements. Then we need to look for changes in a particular person’s levels that would indicate disease. And, ideally, we would have all of that data cross referenced with clinical outcomes. That way, every change could be interpreted in the light of as much data as possible. I think my research can help enable this kind of medical “big data” project.

Sometimes wish I could do this research just because it is cool. Just because I am curious if these particles can be made to talk to one another. Just because I want to see how far I can push the idea of a computational particle entity. I appreciate the needs of medicine, and I want to contribute, but I wonder why our culture seems so reluctant to support pure curiosity?

A few days ago I showed the early results for the spectroscopy demonstration I’m working on for my instrumental analysis class. I passed scattered light and collimated light (using an educational kit from Amazon) through a diffraction grating (also from Amazon) and showed that the results were very different. I posed the question in my vlog for my students: why does the scattered light show up as an image of a rainbow while collimated light shows a rainbow projected onto the paper in front of the grating?

Here’s the answer (if you don’t want to watch the answer in video form). collimated beams create a set of collimated rays of different colors which scatter from the paper.

Scattered light can be seen at different angles through the diffraction grating from the same location, so looks like an image of a rainbow.

For a more thorough explanation, I hope you’ll check out the video.

In other news, a Science News report brought my attention to a hand centrifuge capable of 100,000 rpm. The original paper in Nature from the Prakash lab at Stanford is everything I love about open source science. It’s thorough, beautifully presented, and easily replicable.

I ended up ranting a bit in a vlog about anti-vaxxers. The person who started the current brouhaha was a Cleveland doctor who was advising his online readers to avoid “toxins.” Most of the time, talk of “toxins” is really about a superstitious moral purity. This person has the same superstitious aversion to formaldehyde that some religions have about certain foods. It’s not about physical harm (because harm is demonstrably absent). So it must be about some other principle.

Formaldehyde is toxic at high doses. So is salt. So is oxygen. Formaldehyde is produced at some level by the human body as a metabolite. The question is: what is the dose? Any doctor should know that the dose makes the poison.

Different compounds have different effects at different concentrations. Medical decisions should be made based on data not based on some vague superstition that chemicals are bad.

I gather that he is being disciplined by his employer. That’s something.

Last year, when I taught instrumental analysis, I gave very conventional lectures. This year, I would like to try to build and simulate instruments instead of just talking about them. With that in mind, I bought a light box from amazon that I can use for several projects. I hope to build a spectrophotometer and a fluorimeter at least. Maybe I can also build some demonstration equipment for electrochemistry. Plus, this gives me the opportunity to teach simulation.

I made a short video about my first challenge to my students. I placed a diffraction grating in front of the light from a diffuser in front of a slit. The results was a nice rainbow. I used ImageJ to take a line scan. That’s one way to get to a spectrum.

The optical components need to be locked into place, the distance in pixels need to be calibrated to wavelength, and the sensitivity won’t ever be great, but I think it will be adequate to show some principles of spectroscopy. And it will definitely be adequate to show how light gets transformed to digital data and how that data can be processed.