All posts by jonfwilkins

Remarkable in the NYT Again

So, since the readers of this blog are, like, totally cultured and stuff, I’m sure you all spent Sunday poring over the New York Times Book Review. But, if you did not read the whole thing — presumably because the paper burst into flames when exposed to the searing heat of your intelligence — you might have missed the big ol’ ad Penguin placed there encouraging you to purchase some of their books this holiday season.

Penguin:Holiday

Six excellent books for the young person (say, 7ish to maybe 13ish) in your life who still needs a present, especially if you’re the weird, misunderstood, intellectual-but-still-cool aunt and/or uncle. Of particular note is the book in the upper right corner, Remarkable, by Lizzie K. Foley, who is renowned not only as a middle-grade author, but as the wife of Lost in Transcription blogger Jon Wilkins.

Five Reasons Biologists Should Use Preprint Servers

So, following my previous post, I got some interesting feedback from a couple of biologists who were not completely sold on the idea of posting preprints of your work to the arXiv (or, now, the bioRxiv). Or, rather, they were not convinced that the cost-benefit calculus worked out in favor of posting. After all, as one person pointed out, there are already a bunch of hoops to jump through on the way to publication, what with formatting, revising, angrily cursing reviewer number 2, reformatting, resubmitting, and whatnot. What does posting to a preprint server do for you, beyond adding another step?

Well, it occurs to me that this is probably a question shared by a lot of biologists out there, so I thought I would share the reasons I’ve come up with.

  1. Open Access. You want your work to be available to the widest possible audience, right? When some enthusiastic young researcher is searching the literature, and they stumble across your seminal work on tribble parthenogenesis, you don’t want them getting Spock-blocked by some crappy paywall. Sure, maybe their University has an overpriced subscription to the obscure journal you published in, but maybe it doesn’t. Or maybe it’s a pain for them to access it via the proxy server when they’re off campus. Or maybe this young researcher doesn’t have access because he and/or she is an independent scholar, because they’re actually too smart and creative to work for The Man. Maybe they’ll just scroll down the search results page until they find another paper by your grad-school nemesis — the one who never chipped in his fair share for pizza — and you’ve lost another citation. Don’t let this happen to you! Make sure that your work is freely, and easily, accessible to everyone everywhere.
  2. Speed. You’ve finished your research, you’ve blindly written down the p-value that the software you downloaded from the internet spit out — er, I mean, “double-checked the statistics”, and you’ve written a beautiful discussion section that skillfully implies that your results are going to revolutionize not only your own field, but any field whose scientists have sufficient foresight to follow in your footsteps. But now you have to wait for six months or a year, or maybe longer, before your paper appears in print, and, of course, by that time, even you will have moved on to more interesting problems. If you post to a preprint server, though, your work is available immediately. And, if you make revisions in response to reviewer comments, you can post the revised version there, too. Some journals (e.g., Evolution) will even let you post the final, published, journal-formatted PDF to the preprint server after some time (12 months following publication for Evolution). So, the fact that you’re getting your work out there early does not mean that you’re committing to something less than the final version.
  3. Normalization. At this point, most biology journals are okay with authors posting their manuscripts to preprint servers, but some still are not. Not to name names (*cough* Elsevier *cough*), but some publishers would still like to hold on to an outdated publishing model where they can earn obscene profits through ownership of a product to which they contribute little to no value. The more biologists publish preprints — and commit to publishing only in journals that permit prepublication — the more pressure it places on publishers to stop rent-seeking. Basically, it is a really easy way to nudge the world of academic publishing in the direction of justice. Or, you know, if you prefer, you can keep feeding those paywall parasites like the rest of your Vichy scientist colleagues. No judgment here.
  4. Feedback. When you’re desperately worried about getting out publications so that you can get your degree, or get tenure, or whatever, it is easy to forget the real purpose of peer review. In an ideal world, peer review means that experts in your field look closely at your work and help you to make it better. By posting a preprint, you are able to get comments from the entire community — at an early enough stage that those comments might actually help you to improve the paper before it fossilizes.
  5. The Left Side of History. Look, the fact is, this is the direction that everything is moving. And you need to ask yourself, years from now, do you want to be the stodgy, old, out-of-touch professor who doesn’t post preprints, and who has to get their grad students to help set their powerpoint presentation to full-screen mode? Or do you want to be the super-cool hipster prof, who could say things like, “I’ve been posting on bioRxiv since you were in diapers”, but who would never actually say that, because it would make you sound like a total dickhead? At future Thanksgiving dinners, do you want to be your field’s Liz Cheney, or its Mary Cheney?*

* Answer: You want to be your field’s Lon Chaney.

Enter the bioRxiv

So, if you are a Physicist, or if you know a Physicist and are very patient, you’ve heard all about the arXiv, the preprint server that kicked off the open-access publication movement. If not, here’s what you need to know. The idea is that when you write up a paper, you post it online, where it becomes immediately and freely available to the world. If you revise, you can post the revised paper. And, even if you go on to publish the work traditionally, there will be a version out there that is not behind some journal’s paywall.

Most arXiv users do, in fact, go on to publish their work in traditional, peer-reviewed journals. But by posting to the arXiv first, you get your work out quickly. If you’re a naive idealist, this lubricates the flow and speeds the creation of knowledge. If you’re a paranoid careerist, it allows you to date-stamp your ideas to guard against being scooped.

While the arXiv has a “Quantitative Biology” section, preprint culture has never really taken hold in the Biology community the way it has in Physics. But here’s something that will maybe help to push things in the right direction: bioRxiv, Biology’s very own preprint server! The server features twenty-four sub-fields of Biology, and, as of this writing, Evolutionary Biology is WINNING with eight posted manuscripts.

If you’re worried about whether posting a preprint of your manuscript might interfere with your ability to publish in a traditional journal:

  1. Grow a pair of non-gender-specific gonads!
  2. Look into the pre-publication policies of various publishers here. (And, if you’re planning to publish somewhere that prohibits preprints, rethink your priorities, you collaborator!)

Now get to posting!

Anonymous comes to Montclair

So, a couple of years ago we moved to Montclair, NJ, in part because of the excellent public school system. There was some excitement here last Friday, when some “assessments” were posted on the web in advance of their being administered to students.

There is some confusion (at least on my part), and some conflicting reports about what, exactly these tests are for. They are some combination of:

  1. Evaluation of pedagogical methods
  2. Evaluation of teachers
  3. Evaluation of students

In any event, these tests were supposed to be given starting this week, but 14 of the “more than 60” tests were posted online, which, of course, severely compromises the integrity of the tests. The tests were quickly taken down (although nothing ever really disappears from the internet), and the next couple of days were filled with pretty much what you would expect: outrage and conspiracy theories from parents; defensiveness and corporate double-speak from the superintendent’s office.

Then, today, an Anonymous video went up claiming responsibility for the hack . Suddenly, things get interesting. Go here to watch the video. Go here to read the commentary from Baristanet (the local online paper) — entertaining in part because of the apparent lack of familiarity with Anonymous.

Of course, the usual caveats apply. Due to its open, self-organized nature (anyone can generate an Anonymous-style video), it is difficult to know if Anonymous was actually responsible (as opposed to taking credit after the fact), or what it even means for “Anonymous” to be responsible. However, it takes something that looked a lot like run-of-the-mill bureaucratic incompetence and reframes it as a guerrilla struggle against the corporate takeover of public education.

So, what’s the story then?

Well, now that there’s an Anonymous video involved, I’m going to find out.

This Spam REALLY Doesn’t work right now

So, like you, I get a lot of spam e-mail, much of it some variant of the Nigerian 419 scam.

Here’s the one I got today:

Dear Sir
I want to invest in your country. Anyway, my name is. John Mark from Liberia presently staying in Ghana.Already, I have gone through your profile, and I considered you to be credible and competent enough to handle a big project of this nature,which is the reason why I decided to contact you.
Personally, I would like to go into business partnership with you, so that you can assist me to invest and manage my fund there in your country.
The only thing I am considering is the tax, I don’t know how much tax the Government of your country will take from the funds that I want to invest in your company and I don’t
know if there will be any other requirements from us. I intend to invest jointly with you.
The purpose of this mail is to open up communication with you to enable us know each other as regards to our plan to invest our money properly with you.
God bless you as we will be looking forward to hear from you urgently.
Yours faithfully,

John Mark

Here’s the thing. If you’re trying to scam an American right now, when the government is shut down as a result of a crazy-ass blood feud over Obamacare, and when we are just a couple of days away from defaulting on our Federal debt, when the fiscal practices that led to the 2008 crash have, if anything, intensified over the course of the recovery (which was only a recovery at all for the very richest Americans), you can’t lead with “I want to invest in your country.”

That opening pegs you as a scammer, or, worse, a moron.

Steve Lonegan on Syrian “Others”

So, as some of you may know, we’ve got a special election happening tomorrow here in New Jersey, pitting Democrat Cory Booker, the current Mayor of Newark, against Republican Steve Lonegan, the former Mayor of Bogota. The race got a lot of headlines in the past few days after Rick Shafan, a (since fired) senior staffer with the Lonegan campaign, said that Booker’s communications with a Portland stripper sounded like “what a gay guy would say.” He went on to explain in stomach-churning detail what he (as a representative of straight guys everywhere) would have said to the same stripper. If you haven’t read about it, check it out.

But back in September, we got a recorded phone call from Lonegan, urging us to come to a rally in Montclair against military intervention in Syria. Now, while I doubt that I agree with Lonegan on just about any other issue, I am glad that we found a way not to get involved in another war (even if it was going to be “just” airstrikes).

The American’s-bombing-people-in-Syria issue, is settled, at least for the moment, but there was something telling in the phrasing of the phone message. Here’s my transcript:

America is on the verge of another war, a war we can not afford. A war where we do not belong. I’m Steve Lonegan, I’m the Republican candidate for the United States Senate. Please join me this evening in Montclair at 12 Church Street for our anti-war rally.
We should not be putting our money, our troops, and our nation in harm’s way in a war in Syria that will result in the death of thousands of Syrian Christians, Jews, and Others.
We simply do not belong there. There is no excuse for this war. None. Please send our message to our elected representatives across this state and across this country: “No . . .”

That’s where our answering machine cut off. I assume the message was something along the lines of “No war!”

The interesting part of the message was “Syrian Christians, Jews, and Others.” Hmmm . . .

Here’s my read on this. I have no evidence to suggest that Steve Lonegan himself has anything against Muslims. He might, but I’m happy to give him the benefit of the doubt here.

However, it does seem clear that he is unwilling to say that he is against killing Muslims.

Here’s how I picture the strategy meeting:

STAFFER 1: Okay, it looks like Obama is going to war against Syria. We’re tying Booker to Obama, so we need to come out against the war.

STAFFER 2: But we have to be careful. Killing Muslims is still polling very strong with our base.

STAFFER 1: I’ve got it! We refer to Syrian Muslims as “Others”.  That way we avoid appearing sympathetic to them, and in fact, contributes literally to the “Othering” of Muslims, sensu De Beauvior.

STAFFER 2: We’ve got a mole!

Sadly, STAFFER 1’s body was never found.

SFI MOOC on Complex Systems

So, are you looking to learn something new this fall? Do you want to understand the difference between things that are “complex” versus “complicated”? Have you always wanted to understand what the hell Jeff Goldblum’s character was talking about in Jurassic Park?

Well, you’re in luck! Check out Introduction to Complexity, a MOOC (Massively Open Online Course) being offered through the Santa Fe Institute. The course is being taught by Melanie Mitchell, a long-time member of the SFI community, and a professor of computer science at Portland State University. She taught this class last year, and all of the feedback I heard was very positive. Now, second time around, I assume that any kinks that might have existed will have been worked out.

The course officially started on September 29, but you can still enroll, since all of the material is online. And, it’s FREE!!

Here’s the official course description:

In this course you’ll learn about the tools used by scientists to understand complex systems. The topics you’ll learn about include dynamics, chaos, fractals, information theory, self-organization, agent-based modeling, and networks. You’ll also get a sense of how these topics fit together to help explain how complexity arises and evolves in nature, society, and technology. There are no prerequisites. You don’t need a science or math background to take this introductory course; it simply requires an interest in the field and the willingness to participate in a hands-on approach to the subject.

And here’s Melanie describing the course:

http://youtu.be/z_MlMLom-es

Check it out, as well as the other courses that will offered in the future through SFI’s Complexity Explorer program: http://www.complexityexplorer.org/online-courses

Ellsberg: Snowden was Right to Run

So, this is reposted from Vermont Vigilance:

In 1971, Daniel Ellsberg leaked the “Pentagon Papers” to the press, thereby revealing that the Johnson administration had systematically lied to congress and to the American people about the war in Vietnam. He was charged with espionage. However, those charges were later dismissed following the introduction of evidence of illegal wiretapping by the government.

In yesterday’s Washington Post, Ellsberg wrote an opinion piece arguing that although he had stayed in the US to face his criminal charges, he thought that Edward Snowden was right in his decision to flee.

Why? Well,

Many people compare Edward Snowden to me unfavorably for leaving the country and seeking asylum, rather than facing trial as I did. I don’t agree. The country I stayed in was a different America, a long time ago.

Ellsberg notes that he was released on bail, and was able to continue his anti-war activism while awaiting trial. The treatment of Bradley Manning provides an indication of what Snowden would have faced had he remained in the country. He would have been isolated and tortured. Not waterboarding-level torture, as the US still reserves that for Muslims. But, torture nevertheless, in the form of social isolation, sleep deprivation, etc.

Ellsberg concludes with

I hope that he finds a haven, as safe as possible from kidnapping or assassination by U.S. Special Operations forces, preferably where he can speak freely.

What he has given us is our best chance — if we respond to his information and his challenge — to rescue ourselves from out-of-control surveillance that shifts all practical power to the executive branch and its intelligence agencies: a United Stasi of America.

So say we all, Daniel. So say we all.

Restore the Fourth (that’s an amendment, y’all)

So, here’s another cross-post from Vermont Vigilance:

Tomorrow is America’s 237th birthday. I mean, its 208th 29th birthday! (Lookin’ good, America!)

To celebrate, why not join your fellow Americans in protesting the government’s callous disregard for the Fourth Amendment — the one that protects you against “unreasonable searches and seizures”.

There will be a coordinated set of protests nationwide rallying under the banner “Restore the Fourth”. As of now, there are sixty of them, so there is probably one near you. To find your local rally, go to this site: http://www.restorethefourth.net/

Via reddit, here is a list of other things you can do to get involved and make a difference:

Breastfeeding is now Terrorism

So, this is reposted from Vermont Vigilance — a new blogging endeavor [full announcement t/k].

An article from the New York Post describing an incident where a Belgian couple were kicked out of the Metropolis Country Club in White Plains, New York after Roseline Remans began to breastfeed her infant son. In an all-too-common twist these days, their ejection was accompanied by charges of “terrorism”.

Here’s the story. Remans and her husband, Belgian diplomat Tom Neijens (First Secretary of the Belgium Mission to the UN) went to the Metropolis Country Club and asked if they could eat lunch there. They were told yes, they were welcome to eat on the terrace. When Remans started to breastfeed her daughter, a manager came over and told her that she was disturbing the other people at the club, and that she would have to finish in the restroom.

Now, first of all, for the country club to make this request was against New York state law. Section 79-e reads:

Right to breast feed. Notwithstanding any other provision of
  law, a mother may breast feed  her  baby  in  any  location,  public  or
  private, where the mother is otherwise authorized to be, irrespective of
  whether  or  not  the nipple of the mother's breast is covered during or
  incidental to the breast feeding.

In other words, even if you are a private club, once you tell someone that they can eat lunch in your restaurant, you can not then ban them from breastfeeding there. The NYCLU states:

IN PUBLIC YOU HAVE THE RIGHT:

  • To breastfeed your baby in any public or private place where you have a right to be.
  • This includes stores, day care centers, doctors’ offices, restaurants, parks, movie theaters and many other places.
  • No one can tell you to leave any of these places because you are breastfeeding, and no one can tell you to breastfeed in a bathroom, a basement or a private room.

Whether or not Neijens and Remans knew about the law I don’t know, but they argued that they should be able so stay. So, the club called the police, which led to this response, per the Post:

Detective Scott Harding allegedly yelled, “Close the doors!” and two other diners were told to leave the terrace.

“He was walking as if he was acting in a Western movie,” Neijens said. “He had one hand on his gun, one hand on his Taser.”

Neijens said the officer warned the couple they were trespassing and said some people at the club thought they were terrorists because of their black backpack.

When Remans, on the verge of tears, questioned why terrorists would breast-feed at a ritzy club, the cop allegedly replied, “In Sri Lanka, babies are used by terrorists.”

It is not obvious who played the terrorist card here, but there are two main possibilities:

  1. The club told the police that they had possible terrorists on their terrace — an effective way to punish people for not doing what you tell them to do, even if your instructions are illegal.
  2. The police responded to a request to remove some breastfeeding hippies from a swanky club. When they figured out that these were not run-of-the-mill hippies whom they could push around in the interest of catering to the elite, they tried to cover their tracks with, “Um, because, um, terrorism.”

In any event, it seems clear that someone used a disingenuous claim of concerns about terrorism to enforce certain norms of behavior, in violation of the law.