Russell's Blog

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The Dover Train

Posted by Russell on February 14, 2012 at 4:47 a.m.
Well, it's Valentine's Day again. For all you lucky folks who have someone from whom deserts may be extorted, cheers!

As for me, I'm writing this post for the girl on the Dover train who gave me a funny look. Um... Hi.

Don't know if this will work, but stranger things have happened.

Happy 60th, Mom and Dad!

Posted by Russell on February 10, 2012 at 2:24 p.m.
As is often the case, odd people had odd children. Readers of this blog have no doubt long noted a certain... peculiarity of the author, and hypothesized about the individuals who raised me. I can proudly confirm that they are every bit as odd as I am. Anyway, they both turned sixty in the last couple of weeks (my mom in December, and my dad a few days ago), and I wanted to post a little celebration of our great family tradition of crossgrainedness.

For my mom's birthday, she and my sister came over and slept on the floor of my apartment in Davis, despite the availability of perfectly comfortable and reasonably priced lodgings downtown. For her birthday, we found a fetid puddle of water near Lake Berryessa with some tadpoles in it. She was delighted.

For my dad's birthday, he's celebrating his election to the National Academy of Engineering (the sister organization to the Institute of Medicine. He also got this birthday card from his longtime college friend Bruce Reznick :

Bruce is a professor of mathematics at the University of Illinois. He studies the identities of high-order polynomials. So, this really is the a birthday card only he would think to send.

The moral imperative for Open Science

Posted by Russell on February 09, 2012 at 2:41 a.m.
So, there is this law in Congress called the Research Works Act. If enacted, it would prohibit open access mandates by federal granting agencies. It would end the policy that NIH-funded research be deposited in PubMed, and it would prevent other agencies from establishing such policies. It is a bad idea for a lot of reasons. If you want a elegant dissection of the reasons why the Research Works Act is a bad idea, I suggest Michael Eisen's many posts on the topic.

There is now an effort to boycott Elsevier, the authors and primary proponents of the Research Works Act. I signed the pledge, though unfortunately my name doesn't carry much weight. Last week, my advisor got a little worked up about it, and suggested that scientists should perhaps ignore papers published by Elsevier, and then changed his mind about it after some cogent arguments were raised.

It won't serve the progress of science to ignore new discoveries because we don't like the journals they were published in. However, I do not believe that this point, however cogent, is enough to carry the day. He wasn't suggesting that we ignore the discovery, but rather to ignore the publication. We can, and should, treat publications in closed access journals as illegitimate claims to the scientific record.

I was a little puzzled at first that Jonathan didn't make this point. After all, Michael and Jonathan are often called Open Access stormtroopers. But then I remembered that, despite their passion, storming and trooping are not really in their natures. They lack the necessary highhanded arrogance for those activities. As a physicist who jumped into biology late in my education, it's often been pointed out to me that there is nothing so noxiously arrogant as a physicist moonlighting as a biologist. I try very hard not to be "that guy," but I still get the occasional eye roll. So, just for this occasion, I'm going to uncork a little physicist's swagger by framing the need for Open Access scientific publication as a moral absolute.

Whenever something is unclear, the physicist in me always looks at two things. First, I look at the asymptotic behavior (the extremes), and then I look at simplified models that match the asymptotic behavior. Then I check to see if I've got the right model by looking at how it scales and generalizes to the full problem.

On the continuum of open to closed access publishing, the asymptotic behavior in the closed-access direction is simply not publishing a finding at all. In this case, the moral reasoning is simple (that is not to say universally agreed upon, but simple nevertheless). Take the invention of Calculus, for example. Leibniz, not Newton, was the one who did the work, took the risks, and invested time and effort to bring Calculus to the world. In my opinion, this is what matters in terms of establishing precedence. The more one examines Newton's behavior, the more one wishes to credit Leibniz. I am willing to take the plunge and assert that the precise chronology is irrelevant to the question of apportioning credit. What is relevant is the work of pedagogy.

Publishing in a closed-access journal is secret-keeping. It keeps the information confined among a certain group of people. Combined with copyright, it is a life-destroying secret to anyone who shares it without permission. I think it would be fair to weight the amount of credit according to the extent to which the discovery was shared.

Now I'm going to resort to another irritating behavior typical of physicists; I shall reduce a complicated, nuanced situation to a Gedankenexperiment preserving only the essential features, and then extrapolate the results back to the real world.

Suppose you are making soup for dinner, and you discover that a quart of bleach has somehow spilled into the soup. You immediately tell your family that the soup is poisoned. Nobody eats the soup. Dinner is ruined, but everyone is safe. This is what a normal person would do.

Now let's look at the other extreme. Suppose you noticed soup was poisoned, but you kept it to yourself. You watch your family eat the soup, and they get sick. Only a very, very bad person would do this.

We have a sort of emotional model that lets us make a moral judgement about the behavior of the discoverer in this situation. It's easy to make a moral judgement about the extremes, which is why we looked at them. Now, let's look at the in-between situation.

Suppose instead of announcing the discovery, you tell your son that you know something very important. You demand that he give you something precious in order for you to tell him what it is. Then, after taking away one of his favorite toys, you whisper your discovery about the soup into his ear. Then you tell him he mustn't tell anyone, or he will be in very big trouble. So much trouble that you will take all his toys away and never speak to him again. Then you let your spouse and daughter eat the soup, and they get sick.

The in-between behavior is more unethical than the "bad" extreme! Yes, it's better that one fewer person is hurt, but that is a statement about the outcome, not about the behavior of the discoverer. Selecting the in-between behavior just as callous, but adds cruelty and selfishness.

If you behaved this way, it is clear you would not deserve full credit for your discovery. At most, you could claim one third of the possible credit for your discovery because you only shared the knowledge with one third of the people who stood to be affected by it. Most people would give you much less credit than that. We have many pungent words for people who behave like this which I shall not enumerate.

This scenario is exactly equivalent to publishing in a closed access journal. An author cannot excuse themselves by drawing a distinction between the practices of the journal and their own practices and wishes; by choosing a journal, the author chooses that journal's behavior. There are hundreds of journals with a rich spectrum of behaviors ranging from upstanding and public-spirited to cynical and predatory. Through your choice of journal, you must own that journal's behavior.

Science is a universal human enterprise. When an important discovery is made, it eventually touches the lives of every singe human being. If you keep a discovery secret from anyone, you are behaving reprehensibly. It is only fair that your credit and reputation should suffer as a consequence. It is only fair for other scientists to question the legitimacy of your claim to the credit.

The simple and appropriate punishment for keeping secrets is to always treat the first openly available paper as the actual record of discovery. The fact that someone else may have discovered it first, and kept it secret, is a technicality of interest only to historians. This is what science has always done. I am merely suggesting that we regard secrecy on a sliding scale, and to take into account the role that science plays in the world.

What scientists, especially American scientists, need to begin doing is to take a more pragmatic view of what constitutes a secret. What fraction of human beings on Earth have access to Elsevier's catalog? One in a thousand? One in a hundred thousand? One in a million?

The problem isn't the cost. It's the behavior. If you told both of your children about the poisoned soup, but not your spouse, you'd still be an asshole. If you decreased the number of toys that needed to be sacrificed to have access to the discovery, you'd still be an asshole. If you relaxed the punishment for sharing the secret discovery, you'd still be an asshole. If you shared only a summary of your discovery (e.g., 'some of the food in this house has been poisoned'), you'd still be an asshole.

There is one, and only one ethical way to handle a discovery, and that is to share it freely.

Ultimaker EM leakage

Posted by Russell on February 01, 2012 at 4:06 p.m.
Steven Lucero, the machinist for Biomedical Engineering, just finished building his own (well, the college's) Ultimaker 3D printer. BME is in the process of setting up a pretty awesome rapid prototyping facility, with an Objet Eden 260, a MakerBot and now an Ultimaker. To go with the 3D printers, Steven is also setting up a little electronics lab to go with it. A few weeks ago, he asked me for a shopping list of items that would be useful for electronics hacking, which I was delighted to provide.

One of the things I had to put on my shopping list for Steven was a basic oscilloscope. It's amazing how useful these things are. I've wanted my own o-scope for a long time, and so I happened to have a bunch of low-cost o-scopes bookmarked. Steven ended up buying exactly the one I would have bought for myself, which is sold by Sparkfun (they're sold out right now, unfortunately).

I wanted to see if I liked the software, so while Steven was printing something on his Ultimaker, I put two of the probes next to the X and Y stepper motors to measure the EM leakage.

Like most modern digital oscilloscopes, you can freeze the trace, and save the data as a CSV file onto a USB key. So, here's what the EM leakage from the stepper motors looks like during a print :

Cool, huh?