The Chandler project, Getting things done (GTD), efficient code in the PC and in your life

I started using the Chandler Project a while back and I really liked it. It gives you tickler alarms for things you need to do plus a space for notes. So instead of a calendar where once the date is past, the event is gone, it’s a recurring reminder. It’s like a Jack Russel Terrrier, always jumping around and wanting attention. And every little thing can get recorded in its entries so when the reminder goes off, the appropriate info is at your fingertips. It’s based around the GTD model, which sounded interesting.

Alas, the software is still too slow for me. It’s open source and free, so I can’t complain. And the design is slick, so I hope they continue to refine it. But I can’t wait 8 seconds between when I click and when it responds. I could rifle through a paper cabinet in that amount of time. If you have a fast machine, it’s worth checking out.
But it did get me interested in the GTD mentality. That seemed interesting. I have not read the books yet, but they seem to me to be pretty common sense. There’s a lot there about how to ‘climb the ladder’ efficiently, but I’m not sure it goes as deeply into making sure that the ladder is against the right wall .
Here are a couple of the take-home usefuls from my experience with chandler:
1. Make a home for all tasks and make it a habit to put stuff in there. Be it an inbox, a moleskine notebook, a hipster or a PDA, there needs to be a central trusted place where tasks go. If you are spending mental cycles keeping track of what is going on tomorrow, next week, and this year, you can’t be fully involved in the task at hand. Call this the “bucket”.
2. Weekly, but not much more frequently than weekly, go through and decide what the priorities and goals of the next little while should be about. Don’t waste time on thing that are just urgent, make sure that they are also important. Consider the big picture. Go through the incubator.
3. Make a routine of de-cluttering your bucket. Whenever you hit a lull, (i.e. after a meeting, after a class, whatever) go through the bucket. Delegate those you can delegate. Perform the 2-min tasks that are important. Delete things that are not important. Schedule the important things that have a particular day/time into some device that will beep at you when it’s time. Finally, collapse all projects (open loops) into one, immediate, manageable task (plus a note to determine the next one after that). If there are other things concerning that project that are not next but need to be noted, file them with the rest of the notes on that task. If there’s something long-term that is not a task, file it in an incubator file. Everything that is not a next task on some open loop (project) should be gone. That’s brainspace you don’t need to be taking up.
4. Go to the top of the bucket again. Do that thing.

5. Repeat
Sometimes you won’t feel like doing that thing. We’ll address that tomorrow.
-Peter

jerks, leadership, and the consequences of living, or relationships and trust – Part 2

Continued from Personal interactions, management, relationships and trust – Part 1

“Do you know what makes people decent?Fear.”It’s a line from a speech in Dogma, that Kevin Smith movie that inspired protests from lots of religious people who didn’t watch it.The point of the speech is that people only behave well when they are afraid of the consequences of behaving poorly.I wrote a post a while back on the ways that people can motivate other people, and fear underlies all of them.

I had an experience today that made me think that some people have been privileged in their interactions with other people.They have always been given the benefit of the doubt.They have always been treated fairly.So when something annoys them, they have no fear of the consequences of speaking up.Because they don’t know that there could be consequences.

I am absolutely aware that any request I make, no matter how innocuous, has an impact on the relationship.If I am annoyed at something and I ask for it to stop, I have implied that I find someone annoying.That will have consequences.Maybe they will be consequences that I will see, or maybe they won’t be visible, but they are out there. No way around it.

Take this example.The neighbor comes up to the door and says, ‘would you turn your music down?’

The normal person gets a little annoyed.It’s his own radio his own apartment, he should be able to do what he wants… and it is embarrassing to realize that he has intruded on someone else’s space.He wants to keep the peace, though, so he mutters something about not realizing it was so loud or something and he turns it down.

What does the jerk do in the same circumstance?He pitches a fit like a whiny child.And many a time, he will get what he wants.What he wants is to live uninterrupted.And the neighbor goes home, fumes, but doesn’t want to get in a fight, so he puts up with the loud music.And the jerk’s life is uninterrupted without any visual consequences. But this relationship is going downhill.This is not going to become a friendship.

I’ll admit that I find myself really tempted to give the jerk something to fear: a visible consequence.The only reason he acts this way is because it has never blown up in his face. He wants to live life uninterrupted, but he doesn’t deserve it.He’s not entitled to it.Maybe a painful interruption would be good for him.But that’s not high level interaction.Sure, maybe his behavior would improve if he ran into someone who was as big a jerk as he was.Maybe if someone really hurt him for not being polite, he would think twice about being impolite from then on.But probably not, and I don’t want to be the jerk whose job it is to find out.

-Peter

prions, mad cows and memes

Years ago, when I was in school, there were two sources of transmissible disease: bacteria an viruses. This idea was so well entrenched that it was very hard to suggest that there might be a third category. Of course, congenital disease and poisons cause disease, too, but these are nottransmissible. In the last 10 years, a new kind of disease-causing element was isolated: the prion. Even 5 years ago it was a contentious issue, but my sense of the landscape is that the consensus has been reached: there are proteins that mis-form and then cause other proteins to mis-form.

It’s known that these proteins get from one animal to another through cannibalism. If a mad cow eats another mad cow, it spreads the disease. How the mis-folded proteins get from the gut to the brain remains a mystery as best I have heard. I’d be really interested to learn of new findings in that area. In any case, there were some rumors in 2004 that there might be a more virulent form of prion disease in caribou, but I never heard any more about it. Interesting trivia, prions and some spider silk proteins are both amyloids.

I ramble on about this to illustrate a point: extremely unlikely things (flukes) can have a strong impact if they are in an environment that is “propagative”. I’ll illustrate with a flower analogy then talk about prions again. Let’s say I have a hundred acres of fresh, beautiful, irrigated, tilled soil. It’s ready for seed, but it’s in the middle of a desert and there are no seeds. It’s isolated. The event of a single seed (the size of a grain of sand) falling in that huge hundred acres would be impossible to notice. If you looked for seeds with a magnifying glass, you could look for your whole life and never see one land. But if you just wait and look for flowers, you have a much better chance of inferring that a plant has landed. Probably if a seed lands you won’t notice. You might not even notice the first plant. But given a few growing seasons, you will see a whole patch of earth covered with all of that one seed’s great grandchildren. The event was rare, but its consequences grow very quickly in that fertile ground.

Now let’s return to prions. The seed is a single protein molecule mis-folding. It causes other proteins to mis fold. That means that the fertile ground upon which this seed has fallen is the cow’s brain. And the plant that grows is madness. If cow’s brains are isolated, that’s not a big deal for anyone but that cow. But if the cow’s brains are brought into proximity to other cow’s brains, then that one seed (no matter how rare) will take up the whole space eventually.

Eventually, I’d like to talk about memes on this space. Memes are like flowers and prions and seeds. Given fertile space, they spread. The consequences of that are entirely dependent on the type of meme. Some are beneficial and some are detrimental; some are slow to grow while others spread quickly. They are ideas that jump from one mind to another. As humans, we can choose the memes for which we make our minds a habitat. That is one of our greatest gifts.

More to come.

-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.

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

spider silk proteins, microfluidics, and cool stuff that is small

A pair of German groups collaborated to produce an artificial spinarette. They made very small tubes (called Microfluidics by those in the business) into which they injected engineered spider silk proteins produced in bacteria. The obvious cool tings aside (e.g. arachnoweave armor) there are several interesting scientific oddities. The first is in the aggregation of protein eADF3. According to the article, at low concentrations it forms aggregates. But if you add shear flow (like forcing it through a small channel or a spinarette) it makes fibers instead of particles. That’s pretty strange.
Here’s something else. The protein aggregates in salt water under static conditions into tiny particles. These particles unfold and dissolve in pure water. The the fibers made of the same stuff in the same conditions stable in pure water. Something pretty drastic has changed about how those proteins are structured when they assemble under the shear conditions in the flow of that microfluidically confined stream. Indeed, spectroscopy shows a high beta-sheet content of the fibers, although I didn’t see anything about the beta-sheet content of the particles.
But these authors go one step further. A two part mixture of two silk proteins, both found in spiders (the above mentioned eADF3 and another, eADF4) produce a twisted fiber of higher strength and similarity to the natural product of a spider. If you’ve ever watched a nature show and seen a spider at work, you’ll know that they have to pull the silk tightly when they are spinning in order to make it strong; this explains why. The shear forces of the fluid moving through the spider’s little orifice are really important. Maybe that’s another step toward that arachnoweave armor. That and that d3o stuff (like a d3o Hat to protect your head) would make a product fit for Batman.

It’s not recombinant spider silk, but the D3O videos are worth looking at, if you have not already.

-Peter