Tag Archives: chemistry

The difference between utopia and dystopia is doing the dishes

I believe in public funding for science and especially revolutionary, high-risk/high-reward projects.  Most of those projects will fail. That scares the funding agencies. It looks like a lot of wasted money. But I think that’s the price for innovation.

2017-03-23 07_07_42-Krita

We need to fill the beginning of the pipeline with lots of good ideas. When something works, there will be plenty of motivation to move it down the pipe. There are big rewards at the end of the pipe. I think that’s great. I just want there to be more support at the beginning.

For projects that do have support (and not necessarily government support), I also see the little human weaknesses as a real problem holding back important projects. The two projects that come to mind are Open Source Ecology and Paul Wheaton’s Permaculture community.

This article (brilliantly titled The Post-Apocalypse Survival Machine Nerd Farm) reminded me of what it was like to live with roommates. Not everyone is equally motivated. Not everyone wants to volunteer their hours getting up early to build a DIY tractor. And not everyone knows that about themselves. It sounds amazing: sustainable agriculture, technical puzzles, building great things, sharing new technology with the world… Utopia! But the reality is pooping in a bucket and getting up at 6AM to troubleshoot a burst hydraulic line.

The Permies community ran into a similar issue. The Wheaton Labs Farm invited a bunch of people to come out and live and plant and experiment with sustainable agriculture. But people didn’t want to do dishes or do the hand towel laundry. A lot of the unsustainable parts of our culture are a direct result of our coping with these little irresponsible things. Why use paper plates and paper towels? Because nobody wants to take care of the dishes and laundry.

The bottom line is that there are natural resources and technology… but getting people to cooperate and do the unpleasant work is the hard part. That’s no surprise, I suppose. It’s just funny that the difference between utopia and dystopia… at the micro level… is  doing the dishes.

 

 

You are what you eat; exceptions to the rules

This chestnut will appeal to the vegetarians. But we should all be aware. It turns out that when your mom told you that you are what you eat, it was more literally true than she probably believed.

Generally, what you eat gets broken down to rather small molecular bits, then built back up into the stuff that you are made of. Despite the fact that both cows and humans have hemoglobin, we don’t just use theirs. When we eat beef, we break down all the cow protein (including hemoglobin) and then build our hemoglobin from the bits.

There are some exceptions, it seems. As covered in a short news piece by Science, the article published in PNAS details the results of a trio of researchers who dosed themselves with pig-gland extract in order to show that a a sialic acid called Neu5Gc (made by pigs but not people) ends up in human tissue.

Since this molecule tends to attract the attention of the immune system, that’s probably a bad thing.

The Big Upshot for today is this: in biology (and in medicine) there are always exceptions.

-Peter

Modular designs, microfluidics, fab lab and rep-rap

I saw today that in the journal “Lab on A Chip,” Rhee and Burns published a new design for modular microfluidics. Microfluidics has been my life for the last 5 years. I think I’ve mentioned it at some point. It’s been an interesting way to go about science and I’m glad to have been doing it. I can see how lots of projects would be easier if people knew how to use these techniques.

It’s a lot like programming, actually. If you have a problem in the digital world, and you solve it with a clever program, then you’re good to go. It’s easy to repeat it, and you can share the design easily, and the next person who uses it doesn’t have to learn the same level of skill. That’s key: once a programmer gets something to work, it’s a program. The next person just has to run it.

I don’t know if the magic of that is clear to people. Imagine if you were a blacksmith. You train for ten years, build your shoulders, learn the dark luminous secrets of molten iron. Then you can make amazing things like the gate to the winter palace in St. Petersburg. Now let’s say you want to be able to share that ability. You can’t just post it on the ‘net. You can share some ideas, maybe a 10 year curriculum that would help develop the skills… but the skills are not transferrable.

These days, if you have an idea and you write it into code, and you post it on the net, anyone can do what you did. With a click. No practice is required. But what about other, more physical things? In the next while, if Gershenfeld is to be believed, we are going to see material things produced by open source software. The RepRap project is gaining some momentum already. But in the microfluidics arena, a certain kind of open source physical goods is already there.

People publish designs and those designs can be reproduced by people who have only limited training in things like fluid mechanics, lithography, and cell culture. Once produced, they open whole avenues toward the data that was once only obtainable by people with years of skill and training. And it will only get better.

How does modular microfluidics fit into this? That’s another step toward anyone being able to build these devices. A number of user facilities will generate the master for replication molding. Once generated, that master can be used to produce hundreds of the modules that the paper describes. Once produced, these modules are like toy bricks: they can be used to produce anything, from automated, computer controlled chromatographs to microeractors.

I suspect that in 10-20 years, the complex synthesis for all kinds of substances will be reduced to a set of a few of these blocks (or something like them). I can imagine that, in principle, anybody could take a simple instruction set, have their RepRap print it, hook it up to their computer and have it produce LSD from a few household chemicals.

How will that play out, legally and socially?

-Peter

Heparin, analytical chemists to the rescue, and how bias could hurt open science

I was really impressed by the science that tracked down the problem with the contaminated heparin. It made me think of the enormity of coming up with good data in contentious issues like this. I have to wonder what this kind of issues a loaded question like “is this heparin contaminated?” would present for open science.

For people who are unfamiliar, heparin is a drug derived from meat animals that prevents blood coagulation. It’s really important for dialysis patients because in dialysis, blood is passed through a machine to remove the wastes that would usually go out as urine. The machine doesn’t like coagulated blood, an your body doesn’t want the coagulated blood back. So it’s important that it stay un-coagulated. Given that, heparin is pretty important. A bunch of people got sick taking heparin recently (66 died, sadly) and it was up to the analytical chemists to figure out why. It turned out that an impurity was causing the adverse reaction, but the impurity was so similar to the real heparin that it was being missed by the usual tests. In fact, thee have been some allegations that the impurity was deliberately introduced because it is cheaper, and in standard tests will show up as the legitimate compound.

heparin structure diagram from wikipedia
So, to get this figured out, the FDA did something clever. They gave a bunch of samples of the questionable heparin and the good heparin to some analytical chemists, but they didn’t tell the chemists which was which. Two groups of chemists looked for a contaminant and found the same thing independently. The fact that they both found the same impurity in the same sample is good evidence. But without knowing in the first place which sample caused health problems made the conclusion all the stronger.

But I would like to point out that this kind of science is hard. We’re looking at a lot of work, yes. But in this kind of business, it’s so murky and so easy to be biased that careful people need to blind themselves to the facts that might affect their interpretations. I’ve been reading a lot about open science recently, and I think it’s a marvelous idea: share data the way people share code so that the maximum good can come from whatever work people are doing. The problem with the idea is that whole “science is hard” thing. If people start sharing preliminary data, and they have biases and they share these biases, we could end up with open sciecne discrediting itself pretty fast. Unlike broken code that just doesn’t work, broken science can persist for a long time. It would be a shame to see something so promising become the home of charlatans and the self-delusional.

-Peter