Christian Specht wrote a short, cute analysis on citation mutations. He has a follow-up. Basically, these result from typos by authors or typesetters. This isn’t the problem. The problem is that some typos are inherited. Specht speculates that the inheritance  (i.e. copied and propagated through citations in other papers)  is a  problem because it implies that authors simply copy old references from other papers. I guess the ideal would be that authors would use their own database references or to build up their citation from the actual paper.

I ‘m not sure if this problem is as distressing as Specht writes, although to be fair he isn’t exactly worried.)  He simply made a point that there is likely much copying of old references – even if we can’t detect the occurrence because most people usually copy the correct reference.

Specht worries that the incorrect references may be an indication that scientists do not always read the papers they cite. I would add, simply, that maybe some scientists are lazy; if a paper already contains a properly formatted bibliography for the journal to which a new paper is being submitted, I can see why some authors might simply save time and make a copy.

Or the level of scrutiny for a paper usually doesn’t reach into the bibliography, which, ideally, would involve the authors actually searching for  each paper and actually checking if the page numbers match those from the article.

 

http://www.badscience.net/2010/10/degrees-of-consent/

A look at the way science is done, with scientists taking advantage of the indigent and those without health insurance or access to doctors (mostly by the doctors offering some health monitoring in exchange for becoming guinea pigs.)

Hat tip Brenda Wallace

A press release from Queen Mary University of London:

Professor Lars Chittka from Queen Mary’s School of Biological and Chemical Sciences said: “In nature, bees have to link hundreds of flowers in a way that minimises travel distance, and then reliably find their way home – not a trivial feat if you have a brain the size of a pinhead! Indeed such travelling salesmen problems keep supercomputers busy for days. Studying how bee brains solve such challenging tasks might allow us to identify the minimal neural circuitry required for complex problem solving.”

The team used computer controlled artificial flowers to test whether bees would follow a route defined by the order in which they discovered the flowers or if they would find the shortest route. After exploring the location of the flowers, bees quickly learned to fly the shortest route.

 

Some interesting book reviews: Lee Smolin reviews Roger Penrose’s Cycles of Time, in which Penrose speculates about how the universe got its start. The mind-bender is that there might be no such official beginning, at least for our universe. Shame on me, although I am aware of Roger Penrose’s work, I had no idea how significant an impact he has had in physics. As Smolin writes in Nature,

We should pay attention because Penrose has repeatedly been far ahead of his time. The most influential person to develop the general theory of relativity since Einstein, Penrose established the generalized behaviour of space-time geometry, pushing that theory beyond special cases. Our current understanding of black holes, singularities and gravitational radiation is built with his tools.

 

In the same issue of Nature, Jascha Hoffman reviews Charles Seife’s Proofiness, where Seife creates a “taxonomy of statistical malfeasance”.

***

 

An interesting paper in Nature: a comparison of unique human genomes. The 1000 Genomes Project Consortium sequenced 882 people, with varying degrees of coverage (i.e. total nucleotides sequenced.) This has to do with time and costs. There were 2 mother-father-daughter trios who were sequenced with high-coverage, 178 individuals sequenced with low-coverage, and 697 individuals had only coding sequences within their genome sequenced. This type of research will enable researchers to categorize the genetic differences between closely and distantly related individuals. Further development of individual genome sequencing may enable both disease likelihood calculations as well as possibly tailoring drug treatments for disease, finer scale look at population migrations, and genetic correlates of phenotypic variation. Finally, the identification of the single nucleotide changes (polymorphisms) between individuals will also help researchers expand on the number of markers that are linked to a disease (and in fact have already guided researchers in expanding the probes in microarray chips that detect these new markers.)

A second interesting paper, this one published in Science. Workers were able to identify a specific neural circuit, in zebrafish, that processes visual information. Specifically, this circuit is tuned to small objects, perhaps used in the capture of the zebrafish’s prey.

Joe Posnanski coined a term, e-migo, to describe Internet based acquaintances and friendships. I will present blogs from 2 e-migos here.

Jeff Kirvin and Mike Cane have been blogging about mobile technology, content production, and content consumption for some time. They interested me to begin with because they concentrated on ebooks and writing, even before 2000. Kirvin started a Yahoo and then later Google group called “Writing on Your Palm”, ostensibly to discuss technologies for writing. Before Kindle, Nook, iPhone, and Kobo, Kirvin and other enthusiasts have been reading on our Palm Pilots* for over a decade. We used to get our books from Peanut Press in a DRM’ed container format originally designed for PalmOS. Peanut Press later became eReader, which in turn was acquired by Fictionwise. Barnes and Noble bought Fictionwise, took the technology and ported it to the Nook.

* In this history is the main reason for why I just can’t get into e-ink readers (like the Kindle and Nook). I started reading on my Handspring Visor, which was a Palm Pilot knockoff. The screen was black on green, and it looked worse than it sounds. The contrast was low, and there was only so much one can fiddle with to improve the visual quality. Regardless, my point here is that e-ink still does not provide enough contrast for me. As soon as I could, I upgraded to color screens with increasing resolution, from my Visor. I’ve never looked back; I love reading black text on a true white background. The drop-off in readability when I go outdoors is something I can live with and can be ameliorated by cranking up screen brightness. The e-ink screens are still too low contrast for my tastes.

Kirvin has since moved on to a new domain space. He is a writer of fiction and tech; he also blogs a fair bit about the writing process. Part of it seems painful, trying to shape his vision to match his vision. He has a few insights into technology and writing on mobile platforms, which, luckily, isn’t impaired by whatever ails him in terms of publishing fiction.

He noted a recent appearance by Rob Dickins, former head of Warner Records in the UK, who suggested that lowering prices can be a tool to combat piracy. Industry insiders are appalled at the very idea of selling digital content cheap. Like a music album for $2 cheap. Paul Quirk noted that Dickins is making this suggesting after making his money during the halcyon days of $20 CDs. Jonathan Shalit noted that the cheapness of the container will in turn devalue the contents within. That is, selling an album for $2 will give the perception that the music isn’t worth anything more than pocket change. Thus the art is no longer art, but something disposable. Dickins responded in a comment on Music Week (hat tip: Nate Anderson):

Unfortunately Paul is reacting to headlines and rather than serious debate, is speaking in sound bites My point addressed online albums of which we all know has around 80% piracy and by bringing the price down to a ‘non-decision’ payment, I believe piracy could be countered to a degree but more importantly it would bring in the enormous peripheral buys This would allow physical albums to be developed to really give the fans something special at a much higher price points as illustrated by Nine Inch Nails ‘Ghosts I-IV which would make the retail experience much more interesting to the consumer and the retail outlook more positive My worry is that we are seeing an erosion of prices rather than radical decisions……erosion is a passive way to fade out whilst radical thinking is a way to actively build an exciting industry for the future rather than clinging on to business models which are failing us Music has billions of consumers and I for one want to see albums selling tens if not hundreds of millions on a regular basis

My sympathies are with Kirvin, Dickins, and author Joe Konrath, who made a similar argument as Dickins for lower ebook prices. I think Shalit’s analogy is weak, but I think the fact that some people think it makes it something one needs to address and not ignored. In part because these people will need convincing before they release their content. I know each successive generation will lead to a gradual push along the lines of cheap and open ‘content’, but there are backlists I want access to, and before I die, thank you very much.

My snide comment is this. What if the elitist snobs truly think that art will be devalued with the advent of cheap prices? What if they realize that, assuming the $1 book or movie or music album comes, not all artists will get a boost? How depressing would it be if the bump in sales resulted in more units sold of schlock fiction and not, oh dear, literary fiction? What a blow to egos. </snide>

I would love to see the relative sales numbers from iTunes, to compare the distribution of sales across artists. It would also be lovely to see how that compared to the distribution of CD sales of the same artists (and I suppose Amazon would be in a great position to make this analysis.)

Another e-migo, from Palm Pilot days, is Mike Cane. He is a… passionate advocate of technology as a tool of consumers, not producers. Under the cruft, he wishes for easy access to authors’ works because, you know, he wants to read them. He also wants to make things simpler for writers to publish.  Having a publisher dictate to a consumer where, when, and how he should read is obnoxious.

On a final note: I detest how authors, publishers, and critics contribute to the schism of literary and genre fiction. I think that’ is why the argument about devaluation of a books metaphysical worth based upon it’s cheapening monetary value irks me. To me, the point of being an artist, more so than any manufacturer, is to bring a work to market. We will always need food, cloth, nails, hammers, screws, bricks, and wood. Books, music, movies, TV shows, paintings, and sculptures are luxury items. They provide respite, no matter how temporary, from the difficulties of our lives. But we do not need them.

That is why Oprah Winfrey’s first go around with Jonathan Franzen struck such a wrong note with me. If Franzen is a true artist, he would want his works disseminated. It is strange for his clique of snobs – and that is what these authors,  publishers, and critics are – to try an limit access to literary works. Just be glad the Winfrey gave you press and made your books approachable. If an artist has something worthwhile to say, he would want as large an audience as possible.

Forget about monetary gain; I had thought that the satisfaction of creating ideas and having people attend to them is the ideal.  What does it matter if Winfrey is the one who led her audience to the work? If writers were snobs, I would argue that gives them all the more reason to suffer Winfrey’s attention. She would mediate the writer’s experience with the proles, and he will have a soapbox to help (I would go so far as to say teach) readers understand the themes in his works better.

From Creature Cast comes a post about bower birds constructing Ames rooms in the wild. The blog is updated by members of Casey Dunn lab at Brown. (Hat tip: Maggie Koerth-Baker of Boing Boing.)

My life (I am an American male) does not revolve around sports. I do follow the Boston Bruins, but they are never must-see TV for me – even when they are in the playoffs. Sorry, I prefer reading, making sure my house is in order, and spending time with family and friends.

My interest in sports run along mathematical lines; I am more interested in statistical analysis and model building than in the games (and especially for baseball.) That and drinking beer while watching games.

So it is strange that I read just about everything Joe Posnanski writes. He writes about baseball, and without exception I  read his pieces about living and long-dead ball players whom I have (mostly) never seen.

This piece is particularly good. The way I would approach describe Posnanski is that he is about nuance. Nick Hornby isn’t the first to notice that males tend to love ranking things. Bill Simmons and Chuck Klostermann have also made similar points, in their own entertaining ways. Posnanski, in addition to offering his own rankings, a number of observations that tempers the ranking. In other words, the separation between 2 players may not be as large as the gulf implied by, for example, a “first” and “second” ranking. This is interesting and somewhat in contrast to the approach of most sports columnists.

At any rate, here’s the nuance: Ryan and Suzuki are the best at what they do, but they don’t rank among the best baseball players ever. I won’t repeat Posnanski’s arguments here, but he’s not out to trash either guy. He’s simply trying to work through and present an informed opinion and analysis. The pair, Ryan and Suzuki, can be considered exceptional players along one-dimension. Ryan threw more strikeouts than anyone; Suzuki is a hit machine. But because of other inefficiencies in their game, they actually do not help their teams as much as one might think (in terms of preventing runs for Ryan and driving the offense for Suzuki.)

The greater point is this: I think Posnanski is among the best writers in explaining numbers to an audience. In all seriousness, I want that talent in describing science to non-scientists. When Posnanski gets rolling on presenting statistical arguments for baseball excellence, I applaud the effort because he is able to note all the ways in which these “binary answers” have many shades of gray. When Posnanski talks numbers, I don’t see a difference between him and a scientist who is trying to explain ideas to laymen. And of course his writing talent makes you want more. Or at least it makes me want to read more.

I was both disappointed and heartened by the Ben Mezrich book. I had seen The Social Network over the weekend, before starting to read the book. I was surprised by how closely the movie followed the book. The chapters are short scenes, perfectly adaptable to the big screen. I have pointed out before, in an essay on Bringing Down the House, that I’m unsure as to Mezrich’s source work. I’m not accusing him of fabricating the story, but this book, like his previous books on MIT gamblers that I have read, is a narrative history that  focuses on the tale, not necessarily the history, of Facebook.

My disappointment was in Aaron Sorkin. I had attributed the pacing, dialogue, and structure of the movie to his writing. I remain a fan of Sorkin’s Studio 60, so I know that he’s a good writer. I was just disappointed here that I couldn’t attribute the quality of the screenplay entirely to Sorkin.

I was also heartened, because when movie producers desire, they can actually capture the complexity of a book onto screen. It helps that Mezrich writes in movie style. His writing focuses a lot on the characters and atmosphere – again, this idea of scene building, less on what happened (if he did that, Accidental Billionaires would have lasted about 20 pages.) The book is also without frills, the details that add to the richness of the novel. I would have expected a true history of Facebook to focus on the similarities of Harvard Connection and TheFaceBook and whether Mark Zuckerberg intentionally held back Harvard Connection so TheFaceBook would be available first. It might also merit a comparison to how other companies like PayPal, Google, and eBay began. But, Mezrich focused simply on the sex, money, genius, and betrayal.

In this case, I would recommend either the movie or the book. One difference between the two is that the movie is more sympathetic to Eduardo Saverin than Mark Zuckerberg. The book played out a bit more evenly; even Sean Parker isn’t quite the Pied Piper that the movie made him out to be. What Mark, Sean, and Eduardo did all seemed reasonable, even if not rational. Also, some of the scenes are slightly reorganized, but reading or seeing the one is probably enough.