Scientific discourse as an epic FAIL

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How to Publish a Scientific Comment2.pdf (42 KB)
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A post on FriendFeed pointed me to this blog post in Adventures in Ethics and Science discussing a particularly infuriating example of just how broken the current system of scientific publishing can be. The epic tale is presented by Prof. Rick Trebino in a PDF document (below) outlining "How to Publish a Scientific Comment in 123 Easy Steps". This version includes his second addendum in which he gives many excellent (and some painfully obvious) suggestions for how to improve the system.

Here's a preview:

1. Read a paper in the most prestigious journal in your field that “proves” that your entire life’s work is wrong.
 
2. Realize that the paper is completely wrong, its conclusions based entirely on several misconceptions.  It also claims that an approach you showed to be fundamentally impossible is preferable to one that you pioneered in its place and that actually works.  And among other errors, it also includes a serious miscalculation—a number wrong by a factor of about 1000—a fact that’s obvious from a glance at the paper’s main figure.
 
3. Decide to write a Comment to correct these mistakes—the option conveniently provided by scientific journals precisely for such situations.
...
6. Prepare further by writing to the authors of the incorrect paper, politely asking for important details they neglected to provide in their paper.  
 
7. Receive no response.
...
15. Write a Comment, politely explaining the authors’ misconceptions and correcting their miscalculation, including illustrative figures, important equations, and simple explanations of perhaps how they got it wrong, so others won’t make the same mistake in the future.
 
16. Submit your Comment.
 
17. Wait two weeks.
 
18. Receive a response from the journal, stating that your Comment is 2.39 pages long. Unfortunately, Comments can be no more than 1.00 pages long, so your Comment cannot be considered until it is shortened to less than 1.00 pages long.
...
20. Remove all unnecessary quantities such as figures, equations, and explanations.  Also remove mention of some of the authors’ numerous errors, for which there is now no room in your Comment; the archival literature would simply have to be content with a few uncorrected falsehoods.  Note that your Comment is now 0.90 pages.
 
21. Resubmit your Comment.
 
22. Wait two weeks.
 
23. Receive a response from the journal, stating that your Comment is 1.07 pages long. Unfortunately, Comments can be no more than 1.00 pages long, so your Comment cannot be considered until it is shortened to less than 1.00 pages long.
...

And so the saga begins. Really, the whole thing makes my blood boil.


Role models

Over the last month and a half I've had the pleasure of hosting two stand-out examples of responsible parenting. These role models, however, happen to be doves.

At first I was skeptical why a pair of birds would want to build a nest on my front porch, given that we go in and out fairly frequently. To be fair, the rose vines framing the entryway are thick and strong as well as stylish, and few bad guys (except us) would even think of going up in there. They spent a couple of days scoping out the place - I like to think that they were comparison shopping - but in the end, convenience, location, and that je ne sais quoi won out. A few sticks and pieces of dried grass started showing up, and eventually there was a nest.

After a couple weeks I saw a scraggly little chick, but then we went on vacation and it was gone when we came back. I thought maybe I'd imagined it, but the doves were still there, and a couple weeks later there were definitely two chicks. Apparently, doves can have multiple broods in a single mating season, and usually use the same nest. They may even use the same nesting site year after year. So now I knew I was looking at the second brood.

Since I was actually home this time, I watched these guys grow from little pin-feathered ugly ducklings into... well, still kind of ugly but at least full feathered young doves (they had gangly awkward tweenager written all over them). The parents still took turns on the nest but switched more frequently, now that they had two hungry mouths to feed. To eat, the chicks basically stick their beaks inside the parent's and gobble up whatever pre-processed yumness is there. Though interesting, it's really not that pleasant to watch.

The nest soon got a bit crowded as the chicks were almost as big as the adults and would flap their wings haphazardly from time to time. I could sense the parent doves getting a little frustrated and sometimes the male would perch on the branch outside the nest to get some fresh air. The more adventurous chick joined him once (I think he also got most of the food; he was the bigger one). I noticed yesterday that the parents would sometimes both leave the nest, and the chicks would get restless and hop about in the vines.

This morning, I opened the door to find the nest empty. I guess it was time! Maybe the parents will come back and have another brood. If not, maybe next year.

Photos:
1. The female parent, I think. It was slimmer and smaller than the other one.
2. The male parent, I think. Bigger and slightly more colorful.
3. The male on the nest, with one chick visible.
4. The male again, with both chicks getting a little too big for the nest.
5. The big chick sitting with Dad on the branch. The other chick is behind them to the right.
6. Both chicks out of the nest, wondering where Mom and Dad are.

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A community searching for a home

The big news all over the intertubes yesterday was Facebook's acquisition of FriendFeed, a life-stream aggregator and discussion platform. Reactions were all over the place, from "Congrats! This is a great move for you guys!" to "Whatever, it makes financial sense..." to "Oh NoESssss!!! 1 <3 FF!1!! Fb is the worsts!!1!!!11!eleventy!!1!" The move prompted immediate debate amongst the science community and even spurred one member to quit FF 3 hours later, though all the lamenting might be premature. Paul Buchheit, one of FF's developers, assured everyone that FF users and community would be treated right.

Still, it's hard not to let the imagination run rampant with thoughts of a Facebook+FriendFeed frankenstein (FriendBook? FaceFeed? FriendFace?). Sean Percival created a nice mock of what such a mashup might look like (go to his page to see full size):


Jokes aside, there's a chance that whatever solution is presented for current FF users will not satisfy a large fraction of us. For one thing, Facebook is oriented around fundamentally different goals than FriendFeed. Facebook is about connecting to people you share some some relationship with - you went to school together, work for the same company, are family members, etc - and letting them know what's going on in your life, no matter how banal. That's fine, and serves that purpose well. FriendFeed, however, has always been less about who you already know and what you're doing, and more about what you think and what you find interesting. These connections made through common activities and interests online are real and often help initiate connections in the physical world. Facebook, in the eyes of many hardcore FF users, is that awkward high school reunion while FriendFeed is the stimulating group of people you met as part of the XYZ club in college.

Already, a FF group has spawned to discuss the details behind developing an open source version of FriendFeed. It will be interesting to see what they come up with, but just as interesting will be to observe the real-time development of a dynamic grassroots effort.

Cameron also has a great post outlining the differences between Facebook and FriendFeed, and the major directions the science/research community could take from here.

Yet, or not just, another life-streaming service?

On Deepak's recommendation, I signed up for a Posterous account. With FriendFeed and Twitter, plus Facebook which I barely use, I didn't really feel like I needed "yet another life-streaming service". But the benefits I can see Posterous having are:

  1. Posting everything from email and having it all - HTML formatting, tags, embedded photos and video - just work,
  2. A bookmarklet that also allows on the fly post composition with formatting and tags and selected content on the active webpage,
  3. Autoposting to other services I use, including FriendFeed, Twitter, and Delicious

Of course, this being my first post, I don't know empirically if everything will just "work" as they say (for instance, did the numbered list go through from email to post? Update: Yes. However, HTML apparently does not work as I'd originally thought. Gmail's built-in hyperlink formatting probably works, though, and I guess that's the point). Also, I'm aware that you can autopost from other services, but I've found that I don't use them optimally; I think posting through Posterous may make me more consistent. I also think that composing in email comes pretty naturally, and saving takes a lot less time than in Wordpress. Then again, I'm not sure how I would lay out photos using Gmail, since as far as I know, photos are just attached files... and might just be placed at the beginning of the post. Maybe through embedded HTML?

(Update: again, using HTML did not work, but just putting the link to the image inserts the image. I can deal with that.)

Another potential problem might be editing posts. If I post something by email to Posterous, then decide I want to edit or update it, those edits don't automagically appear in the autoposted places (like my Wordpress blog). For things like bookmarks, videos, or photos, I don't see myself editing them much, but if I mean something to be a blog post, I can see that being trouble. So do I not autopost from Posterous to my Wordpress blog, but instead post my blog posts to Posterous later? Does this defeat the purpose?

So we'll see if this is actually more convenient without annoying those who follow me online, or if it just aggravates what is quickly becoming a multiple online presence-onality disorder.

I took the above photo in the new High Line park in New York City's Meatpacking/Chelsea District. Very cool concept, well worth the visit.