Category Archives: PLoS

A run-down of good recent stuff, highly recommended for your weekend reading and bookmarking:
PLoS One: Interview with Peter Binfield:

…In my view PLoS ONE is the most dynamic, innovative and exciting journal in the world, and I am proud to work on it.
In many ways PLoS ONE operates like any other journal however it diverges in several important respects. The founding principle of PLoS ONE was that there are certain aspects of publishing which are best conducted pre-publication and certain aspects which are best conducted post-publication. The advent of online publishing has allowed us to take a step back and re-evaluate these aspects of how we publish research, without the burden of centuries of tradition. In this way, we have been able to experiment with new ways of doing things which may result in dramatic improvements in the entire process of scholarly publication.
The most important thing which has come out of this premise is that unlike almost every other journal in the world, we make no judgment call whatsoever on the ‘impact’ or ‘significance’ or ‘interest level’ of any submission. What this means is that if an article appropriately reports on well-conducted science, and if it passes our peer review process (which determines whether it deserves to join the scientific literature) then we will publish it. In this way, no author should ever receive the message that their article is scientifically sound but ‘not interesting enough’ for our journal, or that their article is ‘only suited to a specialized audience’. As a result, we short circuit the vicious cycle of “submit to a ‘top tier’ journal; get reviewed; get rejected; submit to the next journal down the list; repeat until accepted” and we are therefore able to place good science into the public domain as promptly as possible, with the minimum of burden on the academic community….

The evolution of scientific impact (also a good FriendFeed thread about it):

What is clear to me is this – science and society are much richer and more interconnected now than at any time in history. There are many more people contributing to science in many more ways now than ever before. Science is becoming more broad (we know about more things) and more deep (we know more about these things). At the same time, print publishing is fading, content is exploding, and technology makes it possible to present, share, and analyze information faster and more powerfully.
For these reasons, I believe (as many others do) that the traditional model of peer-reviewed journals should and will necessarily change significantly over the next decade or so.

A threat to scientific communication (read excellent responses by Peter Murray-Rast and Bjoern Brembs and a thread on FriendFeed):

Sulston argues that the use of journal metrics is not only a flimsy guarantee of the best work (his prize-winning discovery was never published in a top journal), but he also believes that the system puts pressure on scientists to act in ways that adversely affect science – from claiming work is more novel than it actually is to over-hyping, over-interpreting and prematurely publishing it, splitting publications to get more credits and, in extreme situations, even committing fraud.
The system also creates what he characterises as an “inefficient treadmill” of resubmissions to the journal hierarchy. The whole process ropes in many more reviewers than necessary, reduces the time available for research, places a heavier burden on peer review and delays the communication of important results.

Why do we still publish scientific papers?:

I agree with the need to filter papers, but I want to be in control of the filter. I don’t want editors to control my filter and I definitely don’t want a monopolist like Thomson to muck up my filter. I don’t care where something is published, if it’s in my direct field I need to read it, no matter how bad it is. If a paper is in my broader field, I’d apply some light filtering, such as rating, comments, downloads, author institute, social bookmarks, or some such. If the paper is in a related field, I’d like to only read reviews of recent advances. If it’s in an unrelated field, but one I’m interested in nonetheless, I’d only want to see the news-and-views article, because I wouldn’t understand anything else anyway. For everything else, titles, headlines or newsreports are good enough for browsing. All of this can be done after publishing and certainly doesn’t require any artificial grouping by pseudo-tags (formerly called journals).

Science Jabberwocky (how to read/understand a scientific paper when you don’t know the technical terms):

I have to confess that in areas outside mine, there seems to be a terrible array of words no more obvious than ‘brillig’ and ‘slithy’. And words that look familiar, like ‘gyre and gimble’, but which don’t look like they are supposed to mean what I’m used to them meaning.

Media tracking:

The theropod behaviour paper that I have been boring you all with this last week or so has been the first time I have had decent control over the media access to my work and by extension the first time I have had a good idea of what happened to the original press release. I know what I sent to whom and when and thus can fairly easily track what happened afterwards to record the spread and exchange of information from that origin. In the past on the Musings I have targeted inaccuracies in news reports of scientific stories but without knowing the exact details of a story (I may have access to the press release but without knowing who it went to). Well, not so this time and as a result the pattern of reporting I can see is both interesting and informative both from understanding how the media works and knowing how to get your own work publicised.

Rapid evolution of rodents: another PLoS ONE study in the media:

Although media attention and coverage is not, and should certainly not be, the only criterion for scientific “quality” (whatever that is!), it is further testimony of the advantage to publish in “Open Acess”-journals in general, and PLoS ONE in particular. This study is also interesting because it shows the value of museum collections as a source for ecological and evolutionary research, a point that Shawn Kuchta has repeatedly emphasized in our lab-meetings (and which I completely agree with, of course).

20 Quick Points from ‘The World Is Open: How Web Technology Is Revolutionizing Education’:

9. Open Access Journals (Opener #5): The publishing world is increasing becoming open access. Open access journals in the healthcare area provide invaluable information to those in the developing world. The Public Library of Science (PLoS) offers free peer-reviewed scientific journals. Scientists who publish in PLoS journals might present their work in SciVee. SciVee allows the user to hear or see the scientist explain his or her research in what is known as pubcasts.

Pedagogy and the Class Blog:

I’ve been using blogs in my teaching for several years now, so I wanted to share a few ideas that have worked for me. I’m no expert and I’m still casting about for solutions to some of the more nagging problems, but after thirteen course blogs spread across seven semesters (I just counted!), I have obtained a small measure of experience. In other words, I keep making mistakes, but at least not the same ones over and over.

Practicing Medicine in the Age of Facebook:

In my second week of medical internship, I received a “friend request” on Facebook, the popular social-networking Web site. The name of the requester was familiar: Erica Baxter. Three years earlier, as a medical student, I had participated in the delivery of Ms. Baxter’s baby. Now, apparently, she wanted to be back in touch…..

Are young people of today Relationally Starved?:

The more I toss it around, I’m not so sure that our students are “relationally starved.” I just think that relationships look much different today than they have in generations past. Their relationships are more fluid and maybe a little more fragile. It is obvious that advances in technology have changed the way relationships are built and maintained (it has for me). This doesn’t mean that children aren’t in need of the same nurturing and love that we might have had, but there are other layers that we need to ask them about. And I think that might be the key, ASK THEM!

The New Yorker vs. the Kindle:

Now, let’s imagine for a moment that we are back in the 15th century, to be precise just shortly after 1439, when Johannes Gensfleisch zur Laden zum Gutenberg invented movable type printing. I can only imagine the complaints that Baker would have uttered in the local paper (which was, of course, copied by hand from the original dictation). What? Only one title on the catalog? (The Bible.) Oh, and the fonts are sooo boring compared to handwriting. And no colors! And the quality of the drawings, simply unacceptable. This movable type printing thing will never ever replace the amanuenses, it will simply die as yet another “modern invention” and things will keep being just the same as they have been throughout what they at the time didn’t yet call the Middle Ages.

The New Yorker & The News Biz:

After many years, I am finally subscribing to the New Yorker again. Not in print, but via their Digital Reader. I’m blogging about it because I like their model: the Digital Reader adds something I wouldn’t get from the library version, and I feel like this new model bears watching as we migrate from print to online.

The psychology of reading for pleasure:

According to a neurological study that Nell performed, processing demands are higher with books than other media (movies, television) but that also means that when you are absorbed in a book, you are more likely to block out distractions. While readers describe being absorbed in a book as “effortless,” their brains are actually intensely active. As one critic said, this is not an escape from thinking, it’s an escape into thinking – intensely, and without distraction.

How Twitter works in theory:

The key to Twitter is that it is phatic – full of social gestures that are like apes grooming each other. Both Google and Twitter have little boxes for you to type into, but on Google you’re looking for information, and expecting a machine response, whereas on Twitter you’re declaring an emotion and expecting a human response. This is what leads to unintentionally ironic newspaper columns bemoaning public banality, because they miss that while you don’t care what random strangers feel about their lunch, you do if its your friend on holiday in Pompeii.
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For those with Habermas’s assumption of a single common public sphere this makes no sense – surely everyone should see everything that anyone says as part of the discussion? In fact this has never made sense, and in the past elaborate systems have been set up to ensure that only a few can speak, and only one person can speak at a time, because a speech-like, real-time discourse has been the foundational assumption.
Too often this worldview has been built into the default assumptions of communications online; we see it now with privileged speakers decrying the use of anonymity in the same tones as 19th century politicians defended hustings in rotten boroughs instead of secret ballots. Thus the tactics of shouting down debate in town halls show up as the baiting and trollery that make YouTube comments a byword for idiocy; when all hear the words of one, the conversation often decays.

Blogging Evolution (PDF):

I describe the general characteristics of blogs, contrasting blogs with other of WWW formats for self-publishing. I describe four categories for blogs about evolutionary biology: “professional,” “amateur,” “apostolic,” and “imaginative.” I also discuss blog networks. I identify paradigms of each category. Throughout, I aim to illuminate blogs about evolutionary biology from the point of view of a
user looking for information about the topic. I conclude that blogs are not the best type of source for systematic and authoritative information about evolution, and that they are best used by the information-seeker as a way of identifying what issues are of interest in the community of evolutionists and for generating research leads or fresh insights on one’s own work.

What Do Mathematicians Need to Know About Blogging?:

Steven Krantz asked me to write an opinion piece about math blogging in the Notices of the American Mathematical Society. I asked if I could talk about this column on my blog, and even have people comment on drafts of it before it comes out in the Notices. He said okay. So, just to get the ball rolling, let me ask: what do you think mathematicians need to know about blogging?

Five Key Reasons Why Newspapers Are Failing and Five Key Reasons Why Newspapers Are Failing, pt. 2:

Journalists are pretty good at working the scene of a disaster. They’ll tell you what happened, who did it, and why.
But when it comes to the disaster engulfing their own profession, their analysis is less rigorous. An uncharacteristic haze characterizes a lot of the reporting and commentary on the current crisis of the industry.
It could have been brought on by delicacy, perhaps romanticism. And since it is not just any crisis, but a definitive one–one that seems to mean an end to the physical papers’ role in American life as we have come to know it–perhaps there’s a little bit of shell-shock in the mix as well.

Online Community Building: Gardening vs Landscaping:

The Gardener creates an ecosystem open to change, available to new groups, and full of fresh opportunities to emerge naturally. The approach is focused on organic collaboration and growth for the entire community. The gardener is simply there to help, cultivate, and clear the weeds if/when they poke up.
The Landscaper creates an ecosystem that matches a preconceived design or pattern. The approach is focused on executing a preconceived environment, regardless of how natural or organic it may be for the larger area. The landscaper is there to ensure that everything stays just as planned.

Don’t Be Such a Scientist: Talking Substance in an Age of Style (book review):

So I end up feeling a bit torn. He’s telling us “Don’t be such a scientist”, and it’s true that there are many occasions when the scientific attitude can generate unnecessary obstacles to accomplishing our goals. At the same time, though, I want to say “Do be such a scientist”, because it’s part of our identity and it makes us stand out as unusual and, like Randy, interesting, even if it sometimes does make us a bit abrasive. But, you know, some of us revel in our abrasiveness; it’s fun.

This has also been in the news a lot last week:
Threats to science-based medicine: Pharma ghostwriting
Wyeth, ‘Ghost-Writing’ and Conflict of Interest
More On Ghostwriting, Wyeth and Hormone Replacement Therapy
Wyeth’s ghostwriting skeletons yanked from the closet
Ghostwriters in the sky
Quickie Must-Read Link … (probably the best commentary of them all).
Several recent posts on the topic dear to my heart – the so-called “civility” in public (including online) discourse:
How Creationism (and Other Idiocies) Are Mainstreamed:

One of the things that has enabled the mainstreaming of various idiocies, from altie woo, to creationism, to global warming denialism is mainstream corporate media’s inability to accurately describe lunacy. For obvious reasons, ‘family-friendly’ newspapers and teevee can’t call creationists, birthers, or deathers batshit lunatic or fucking morons. This is where ‘civility’ (beyond the basic norms of decency when dealing with the mentally ill) and pretensions of ‘balance’ utterly fail.

Weekend Diversion: How to Argue:

You are, of course, free to argue however you like. But if you want to argue on my site, you’re really best off remembering this hierarchy, and staying as high as possible on it. Most of you do pretty well, but this has served me well in general, and I hope it helps you to see things laid out like this. And if not, at least you got a great song out of it!

When an image makes an argument:

Along similar lines to a frequentist interpretation of the strata, maybe this pyramid is conveying something about the ease or difficulty inherent in different types of engagement. It doesn’t take a lot of effort to call someone an asshat, but understanding her argument well enough to raise a good counterexample to it may take some mental labor. If this is the rhetorical work that the pyramidal layout does here, it may also suggest a corresponding hierarchy of people who have the mental skills to engage in each of these ways — making the people at the tippy-top of the pyramid more elite than those using the strategies from lower strata.

How to Argue…:

White men are sufficiently privileged enough to demand that they be treated respectfully while white women, at best, can expect to be presented with contradiction and counterargument. When I saw the category “responding to tone” I thought of the “angry black man” who, although perhaps right, is castigated for his anger and lack of civility for not conforming to the norms of white society. If you’re a non-white woman? Then, the best you can do is hope to not be denied food and shelter if you don’t fuck your husband enough (h/t to Free-Ride for pointing this article out), but you only expect to be part of the discussion if you’re allowed to be.
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The call to civility is a frequent tactic to derail the discussion and is as much of an ad hominem attack as calling someone a cocknozzle. It fails to recognize the perspective of the other party or appreciate why they might be angry.

More on the topic:
Dr. Isis Learns to Argue:

I am lucky to have such thoughtful commenters. When I wrote the previous post I had no idea that bleeding from my vagina was clouding my judgement. Then, just when I thought I had cleared enough of the estrogen from my girl brain to understand, I learned that this was all a carefully planned tactic to teach me a lesson. Damn! I hate when that happens!

Weekend Diversion: How to argue…and actually accomplish something:

Here we arrive at the meat of the matter. Once having accomplished more than about 300 ms worth of consideration of a given topic, people are highly resistant to the idea that their rationale, conclusions and evidence base might actually be wrong. And the wronger the consideration might be, the more resistant to acknowledgment is the individual. We might think of this as the intrapersonal Overton window.

A Tale of Two Nations: the Civil War may have been won by the North, but in truth the South never emotionally conceded.:

The Civil War may have been won by the North, but in truth the South never emotionally conceded.
The Town Hall mobs, the birthers, the teabaggers are all part of that long line of “coded” agitators for the notions of white entitlement and “conservative values.”
Of course, this conservative viewpoint values cheap labor and unabated use of natural resources over technological and economic innovation. It also – and this is its hot molten core – fundamentally believes that white people are born with a divine advantage over people of other skin colors, and are chosen by God to lead the heathen hordes.
That a Town Hall mob is itself a heathen horde would never occur to the economically stressed whites who listen to the lies of the likes of Glenn Beck, Sean Hannity, Rush Limbaugh and Lou Dobbs. Lies that confirm an emotionally reinforcing worldview – however heinous – become truths for those in psychological need of feeling superior and chosen.

I remember an America where black men didn’t grow up to be President.:

And all of them are asking for their America back. I wonder which America that would be?
Would that be the America where the Supreme Court picks your president instead of counting all the votes? Would that be the America where rights to privacy are ignored? Would that be the America where the Vice President shoots his best friend in the face? Or would that be the America where an idiot from Alaska and a college drop-out with a radio show could become the torchbearers for the now illiterate Republican party?
I fear that would not be the America they want back. I fear that the America they want back is the one where black men don’t become President.
I remember that America. In that America people screaming at public gatherings were called out for what they were – an angry mob. Of course, they wore sheets to cover up their bad hair. Let’s be clear about something: if you show up to a town hall meeting with a gun strapped to your leg, the point you are trying to make isn’t a good one. Fear never produced anything worthwhile.

In America, Crazy Is a Preexisting Condition:

The tree of crazy is an ever-present aspect of America’s flora. Only now, it’s being watered by misguided he-said-she-said reporting and taking over the forest. Latest word is that the enlightened and mild provision in the draft legislation to help elderly people who want living wills — the one hysterics turned into the “death panel” canard — is losing favor, according to the Wall Street Journal, because of “complaints over the provision.”

Two oldies but goodies:
Atheists and Anger:

One of the most common criticisms lobbed at the newly-vocal atheist community is, “Why do you have to be so angry?” So I want to talk about:
1. Why atheists are angry;
2. Why our anger is valid, valuable, and necessary;
And 3. Why it’s completely fucked-up to try to take our anger away from us.

Atheists and Anger: A Reply to the Hurricane:

Now my replies to the critics. I suppose I shouldn’t bother, I suppose I should just let it go and focus on the love. But I seem to be constitutionally incapable of letting unfair or inaccurate accusations just slide. So here are my replies to some of the critical comments’ common themes.

The Privilege of Politeness:

One item that comes up over and over in discussions of racism is that of tone/attitude. People of Color (POC) are very often called on their tone when they bring up racism, the idea being that if POC were just more polite about the whole thing the offending person would have listened and apologized right away. This not only derails the discussion but also tries to turn the insults/race issues into the fault of POC and their tone. Many POC have come to the realization that the expectation of politeness when saying something insulting is a form of privilege. At the core of this expectation of politeness is the idea that the POC in question should teach the offender what was wrong with their statement. Because in my experience what is meant by “be polite” is “teach me”, teach me why you’re offended by this, teach me how to be racially sensitive and the bottom line is that it is no one’s responsibility to teach anyone else. And even when POC are as polite as possible there is still hostility read into the words because people are so afraid of being called racist that they would rather go on offending than deal with the hard road of confronting their own prejudices.