Really nice article by Jonah Lehrer on “The Illusion of Streaks” that ties in well both with an earlier post I’d written here, and with an argument I was trying to make in a bar this weekend. The basic premise is that the human brain has evolved in a manner that leads to a distrust of scientific reasoning and a dislike of doing the math in favor of stories. As a species, we tend to impose pattern where there is, in fact, no actual pattern.

Lehrer’s article looks at this year’s NCAA Basketball Tournament, along with several studies on basketball and baseball, and discusses how we perceive players to be having “hot streaks”, when in fact, such things don’t exist. This continues to strike me as a major stumbling block in our scientific educational efforts. Fairy tales and fantasies just seem to work better for the human brain than fact-based reasoning.

Interesting article out in The Economist this week, which talks about the future of social networking, and Facebook in particular. The central thesis is that aspects of social networking will become ubiquitous as time goes on, but that like web-based e-mail, it’s not something that has much of a business model or a possibility for monetization:

Web-mail has certainly not become a business. Admittedly, Google, Microsoft, Yahoo!, AOL and other providers of web-mail accounts do place advertisements on their web-mail offerings, but this is small beer. They offer e-mail—and volumes of free archival storage unimaginable a decade ago—because the service, including its associated address book, calendar, and other features, is cheap to deliver and keeps consumers engaged with their brands and websites, making users more likely to visit affiliated pages where advertising is more effective.

Social networking appears to be similar in this regard. The big internet and media companies have bid up the implicit valuations of MySpace, Facebook and others. But that does not mean there is a working revenue model. Sergey Brin, Google’s co-founder, recently admitted that Google’s “social networking inventory as a whole” was proving problematic and that the “monetisation work we were doing there didn’t pan out as well as we had hoped.”

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Chris Mooney, author of “The Republican War on Science” has an interesting piece online at Science Progress, titled, “Enablers: Sometimes Refuting Unscientific Nonsense Reinforces It”. In it, he argues that time spent arguing with anti-Evolutionists, or Global Warming skeptics could be better used promoting accurate and real science, rather than refuting unscientific information:

“The reason is that if you actually bother to rebut the Heartlands and Discoverys of the world, you instantly enter into a discourse on their own terms. The strategic framing these groups employ to attack mainstream science heavily features the rhetoric of scientific uncertainty–and so if you try to answer their arguments, you’re inevitably committed to conveying more abstruse technical information and, thus, more uncertainty as soon as they wail back at you (which they thoroughly enjoy doing).”

He also notes that journalists love a controversy, so by engaging in arguments, you bring more attention to the anti-science viewpoint. I think he’s right in a lot of ways. So much of the science blogosphere seems to be endless tedious refutations of creationist posturing that 1) I have no interest in reading, and 2) seem to only draw more attention (and higher Google rankings) to that posturing. Obviously we can’t let anti-science forces be the only voice heard, but aren’t there more positive ways we can engage the public, rather than constantly engaging in back-and-forth bickering?

I seem to have been doing a good job of riding the cultural zeitgeist with a recent blog posting, as there have been several writers who have voiced their opinions on their blogs on the subject of reader comments on journal articles. These thoughtful posts are particularly helpful, as I’m giving a talk at a regional Society for Developmental Biology meeting later this month on the subject of online tools and whether any of them are useful. The comments on my earlier talk have been very helpful as well, pointing me toward some great sites like GoPubMed and EpiSpider. I think these mashup sorts of sites, accumulators of information from a variety of sources show great potential. The problem of “I can’t keep up with the literature” is a serious one that Web 2.0 (or whatever you choose to call it) offers relief from. This is certainly a more promising area than yet another “Myspace for scientists” or another Digg clone.

On the subject of readers not leaving comments on papers:
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Good to see Cold Spring Harbor Laboratory Press‘ editor Alex Gann surviving a scandal that’s rocking the biology publishing world. Really, those of us who know Alex were more surprised to see the word “conciliator” used to describe him than we were that he was involved in some sort of sordid affair.

The March issue of CSH Protocols includes a diverse trio of methods for fluorescently labeling cells and subcellular structures. The most basic of the three methods comes from Brad Chazotte at Campbell University and covers labeling of lysozymes with Neutral Red. This joins a group of already-published protocols from Chazotte on labeling cellular structures including the plasma membrane, the golgi apparatus and acetylcholine receptors. Expect more articles in this series in forthcoming issues.

The second protocol provides a method for differentiating viable plant cells from dead plant cells. Contributed by Birgit Schwab and Martin Hülskamp from the Center for Plant Molecular Biology in Tübingen, the technique takes advantage of the inability of propidium iodide to enter live cells. Dead cells allow it in, and fluoresce red, so they can be easily identified.

Finally, Paul Kulesa’s group at the Stowers Institute have written up their method for Photoactivation Cell Labeling for Cell Tracing in Avian Development. This technique allows for selective marking of individual cells or groups of cells at precise times and spatial locations normally not accessible using previous techniques. It’s less invasive than most methods used for labeling cells in avian embryos, and can be targeted to both individual cells, or small groups of cells. This month’s cover image shows an example of this technique.

Kind of an odd editorial in the latest issue of Science. The author, computer scientist Ben Schneiderman coins what he apparently thinks is a new term, “Science 2.0″ (I’m sure he might get a few arguments on that), and defines it as the study of human interactions on the internet. It’s a reasonable enough thesis, that these tools make it easier to study how people collaborate (when using these tools), and it will be an interesting subject. I’m not really sure how relevant it is though, to scientists who aren’t studying human interactions. Researchers need to carefully pick and choose tools that are most likely to be fruitful, to add to their research rather than take away from it by demanding their time and effort. And as Jaron Lanier has pointed out, there are some problems where the group-think inherent to social networks and open collaborations can stifle real progress.

A few interesting articles of note, one on science, the others on the future of publishing:

First, a brutal, but really funny review of a PLOS editorial on advice for graduate students:

“You will be happier if you don’t do things you hate. I must say that this thought never occurred to me before. Also don’t waste 7 years of your life, which admittedly was my first instinct. Good thing I read this editorial.”

Next, Cory Doctorow’s interestingly reasoned take on why stand-alone e-book readers like the Kindle are doomed to failure. He breaks it down in terms of the economics of production, that there simply aren’t enough readers out there to allow the cost of production of these devices to drop (especially when compared with multi-function devices like an iPhone or GameBoy):

“Frankly, book reading just isn’t important enough to qualify for priority treatment in that marketplace. E-book readers to date have been either badly made, expensive, out-of-stock or some combination of all three. No one’s making dedicated e-book readers in such quantity that the price drops to the cost of a paperback — the cost at which the average occasional reader may be tempted to take a flutter on one. Certainly, these things aren’t being made in such quantity that they’re being folded in as freebies with the Sunday paper or given away at the turnstiles at a ballgame to the majority of people who are non-book-readers.”

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The March issue of CSH Protocols has two featured (freely available) protocols on high-throughput methods for studying gene regulation.

The first method approaches regulatory analysis through epigenetic mechanisms. Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation, developed by Marcos Estecio and Jean-Pierre Issa of the MD Anderson Cancer Center, and Pearlly Yan and Tim Huang of the Ohio State University Comprehensive Cancer Center is a rapid, genome-wide method for identifying regions where methylation is occurring. This protocol has proven successful for proven successful for use in comparing normal tissues and tumors, helping researchers better understand the factors responsible for cancer.

The second protocol looks at the binding of regulatory proteins to DNA and their role in transcriptional regulation. The method, DNA Immunoprecipitation (DIP) for the Determination of DNA-binding Specificity, allows researchers to determine the specific DNA sequence that a regulatory protein binds. The technique allows for rapid screening of the entire genome for these binding sites, which gives insight into which genes these protein factors control.