Category Archives: Science

All things scientific

Favorite Links for Week 49 2019

“Water-in-salt” electrolyte enables high-voltage aqueous lithium-ion chemistries

Wow. OK, this is a tour de force. Some of the experiments are pretty typical battery research (voltammetry, discharge curves, etc.). This group went farther and did molecular dynamics and density functional theory analysis of the chemistry happening during the charging process. They do 17O NMR to look at the electrolyte and water. They do XPS and etch and do XPS again to look at the depth profile of the chemistry. If you want to know what’s happening in a battery, here’s how to do it.

OK, stuff that’s not really science below.

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Fitbit can tell when I’m stressed

Fitbit can look at your resting heart rate over time. Minor complaint: I couldn’t download my resting heartbeat data into Excel, though. It’s hard to look back at resting heart rate history. I had to click back through the “date” function in the Dashboard and take screenshots of the graph every ~30 clicks/days. Google bought FitBit recently, and now the high-resolution heart rate data are available to Calico, I expect. That could be a big deal.

2019-11-27 13_27_25-_2019-11-27 10_31_29-Fitbit Dashboard.xcf-1.0 (RGB color, 7 layers) 984x390 – GI

On my graph, you can see the rise preceding major grant deadlines. So that’s… cool? Cool. Cooool.

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Favorite Links for Week 47 2019

Baddy One Shoe – Dear Hank & John podcast

“I’m just there to try and make the other people on Twitter feel better. I know how rough it is out there. I’m trying to help.” Said Hank Green, famous person on the internet. He said this on his podcast, Dear Hank and John, which I have recently discovered. I know I’m late to the party on this one, but it’s fun. The quote reminded me of Jack Torrence from The Shining (re-watched in preparation for Doctor Sleep, which I liked a lot more than Kubrik’s film).

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Favorite Links for Week 45 2019

What is the real, mathematical dog-year calculation?

Ok, so we all knew dog-years can’t be a linear translation to human years. So what is the real translation between human and dog age? There’s an “epigenetic clock” discovered by Steve Horvath. Basically, DNA gets little chemical modifications that help turn genes on and off. It turns out that some of those modifications accumulate with age. And this biochemical signature tracks age better than just about anything else. So is it the same in dogs? And can we use it to correlate dog-years to human-years? Yes. Tina Wang et al. figured it out (bioRxiv).

Personalized predictions of blood sugar based on poop bacteria

This 2019 paper, “Personalized Approach to Predicting Postprandial Glycemic Responses,” showed a predictive model for blood sugar spikes after meals. The composition of the food (carbohydrate content and calorie content) did not predict blood sugar spikes very well. On the other hand, food information PLUS information about a specific person’s gut microbiome did a very good job. So if you knew your gut microbiome, you could make better food choices.

Failure Found to be an “Essential Prerequisite” For Success

These folks used the NIH database of applications for grants to see what differentiates people who eventually succeeded from those who didn’t. The average was two failures before a successful grant application. I wish I could convey how incredibly hard it is to put together a proposal that gets rejected.

Philip Pullman on Children’s Literature and the Critics Who Disdain It

I read this essay a few days ago and loved it. It came up in conversation, too. The premise is that good literature is not accessible literature. That a book is something children enjoy just means that it is clear and accessible, not that it is simplistic. Generally, children don’t like simplistic. And if a book is enjoyable for children and has depth, it will be equally enjoyable for adults.

Atomic Force Microscope was used to look at single molecules and resolve details

The article, “Revisiting Kekulene: Synthesis and Single-Molecule Imaging,” is amazing. First, what a crazy molecule. Second, what an amazing technique to look at its structure and properties.

Little Things:

Can snakes use doorknobs? Wait for it to find out


crystals of potasium phoaphate incorporating the chemical amaranth dye

Amaranth Potassium Phosphate Crystals

Potassium phosphate crystal chemistry

This weekend I grew some potassium phosphate crystals with amaranth dye. I did this back in 2001 in Bart Kahr’s O-Chem class and remembered it recently. It’s a fun demonstration of the chemistry of crystal growth, the different chemistry of the crystal faces, and it’s pretty. I found Prof. Kahr’s paper[1] that gives a “foolproof recipe” and it did not disappoint. Even this fool could make it work.

As the crystals grow, each face of the crystal has a unique topology. The corners are growing with a different spacing of atoms than the faces, and the faces can be different from each other. Sometimes, the faces have the right spacing to allow a dye molecule to stick. In this case, there is a big difference between how well amaranth dye sticks to each face. So as the crystal rows, it only gets dyed in two quadrants.

We can learn about chemistry from crystals

Crystals are super useful to chemists. A good crystal of a chemical can be used to get x-ray diffraction data on the structure of the chemical. The most detailed structures are derived from x-ray diffraction data.

Knowing how molecules assemble into crystals is also really important to materials scientists. If you want to design a material from its atoms, you need to know how they are going to come together. I’ve been working on making an iron battery and reading up on battery chemistry. One of the interesting papers I read talked about designing a cathode material to hold sodium atoms. The chemists designed the “holes” in the structure to hold sodium atoms – and they needed to know how the other atoms would come together to make that shape.

Why chemically dyed crystals are cool

Of course, dyed crystals just look cool. Maybe that’s silly, but if you’re trying to teach organic chemistry, it’s good to have something visual and striking to hold on to. A lot of O-chem is solvents and white powder, so anything that sticks in the memory is a help.

The other reason I think that dyed crystals are so cool is that they dyes can be held still very precisely. One of prof. Kahr’s later papers used a crystal to hold a fluorescent dye in place at a specific orientation. Then they used a fluorescence microscope to look at single dye molecules[2]. I think that’s just really cool. I gather that they are more stable in the crystal than they are in solution.

I also made a time-lapse movie of the crystallization

Instructions (following [1])

  • Dissolve 17 g potassium dihydrogen phosphate (KDP) in 50 ml water with heating. Using a teflon stir bar helps.
  • Dissolve 4 mg amaranth dye in ~1ml of water and add to the mix.
  • Pour into a wide dish and allow to cool and evaporate slowly over ~4-24 hours.


1.Kahr, B. & Vasquez, L. Painting crystals. CrystEngComm 4, 514–516 (2002).

2.Wustholz, K. L., Kahr, B. & Reid, P. J. Single-Molecule Orientations in Dyed Salt Crystals. J. Phys. Chem. B 109, 16357–16362 (2005).