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PeerJ, A New Open Access Megajournal Launches

Mirk Re:mixed signals from science media... (61 comments)

"What on earth would keep a bunch of well funded liars like American Heritage Institute from buying up all the articles they want?"

Peer-review. PeerJ is particularly good on this, in that it allows the whole peer-review history of papers to be published alongside the final version: the original submission, the reviews, the handling editor's decision, the authors' rebuttal letter and revision, subsequent editorial comments, etc. As an example, you can see this audit trail for our own PeerJ paper on sauropod necks.

about a year and a half ago
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PeerJ, A New Open Access Megajournal Launches

Mirk Re:Charging authors is not much better... (61 comments)

I agree that what we really want is a system where the price of publishing is part of the price of doing research. That is what we're moving towards as funding bodies increasingly allow publication fees to be covered by their grants. But even without this, charging to publish is much better than charging to read, because it's a non-monopoly market. When Elsevier charge $40 to read one of their articles, a reader doesn't have the choice of going to a different publisher: no other publisher has the specific article the reader needs. But when they charge $3000 to publish my article I can go to any rival that offers similar services, and find one that instead charges $1350 (PLOS ONE) or $99 (PeerJ).

about a year and a half ago
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PeerJ, A New Open Access Megajournal Launches

Mirk Re:Charging authors is not much better... (61 comments)

Check the PeerJ site. Peer-reviewers are chosen by an academic editor -- standard practice at scholarly journals. There is a board of 800 academic editors (PeerJ's planning to get big, quickly). That large board is overseen by a much smaller senior board to 20 scientists (of whom five have Nobel prizes to their names). It's serious stuff.

about a year and a half ago
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The value of BASIC as a first programming language

Mirk Link in main post is no longer correct (2 comments)

For some reason, Wordpress published this article as though it had been pushed two days ago. When I changed the release date to today, that changed the permalink, if you can imagine anything so dumb. So the link that I submitted is now broken -- D'oh! Please amend to: http://reprog.wordpress.com/2010/03/09/where-dijkstra-went-wrong-the-value-of-basic-as-a-first-programming-language/ Sorry about that.

more than 4 years ago
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Whatever Happened To Programming?

Mirk Re:Misleading summary. (623 comments)

No indeed, Don Knuth has surely never heard of me. Sorry if I gave that impression, I didn't mean to.

more than 4 years ago
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Dinosaur Posture Still Wrong, Says Study

Mirk Author's response to points raised in the comments (226 comments)

I am the Mike Taylor that is the lead author of this study. As pointed out by MaXintosh, the paper itself is freely available from the open-access journal Acta Palaeontologica Polonica, and we urge everyone who's interested to read it for themselves: we kept it short and made efforts to keep it comprehensible to intelligent non-specialists. It's at http://www.app.pan.pl/article/item/app54-213.html

Also, if the article pointed to here is Slashdotted, there is A LOT of other media coverage out there, including a TV interview, seven radio interviews, at least 25 online news sources and at least 14 blogs. Handily, we've linked them all from a page on our own blog, which you can find at http://svpow.wordpress.com/papers-by-sv-powsketeers/taylor-et-al-2009-on-neck-posture/

And maybe best, that blog -- Sauropod Vertebra Picture of the Week -- now has a sequence of seven posts explaining the research in more detail: these too are linked from the page I mentioned, and I think many Slashdotters will find them interesting.

To respond to a couple of specific points that have been raised in the comments here:

1. TinBromide though we compared only with giraffes, but in fact we compared with LOTS of animals, including birds, crocs, lizards, turtles, mammals and amphibians. The result were compellingly uniform. Similarly, MaXintosh wrote that "the authors (of the paper, not TFA) hedge their bets heavily by saying that IF sauropods are directly comparable to extant taxa". Well, sort of: we did rather nail our colours to the mast when we wrote "Can the habitual posture of extant amniotes be expected to apply to sauropods? Phylogenetic bracketing strongly supports this hypothesis as the neck posture described by Vidal et al. (1986) is found in both Aves and Crocodylia, the nearest extant outgroups of Sauropoda, as well as in the increasingly remote outgroups Squamata, Testudines and Lissamphibia."

2. eldavojohn asked "Why are we arguing over which position was the default when it's entirely possible that they utilized both positions" and noted that "There's plenty of pictures on Wikipedia [wikipedia.org] of the animals depicted both ways." It's true, of course, that animals can and do adopt different postures at different times: we make the point in the paper that sauropods had to be able to get their heads down low in order to drink, and could therefore pass through all intermediate postures. What we're talking about here is HABITUAL posture -- they way they spent their time when not actively doing something different. Geese can reach the ground, but they don't spend their lives that way.

3. A few people mentioned the problem of pumping blood up a high neck to the brain. We can't say too much about this at the moment as we're working on a paper on this subject and don't want to scoop ourselves. However, we do have good reason to think that the blood-pressure problem is not so severe as it's been depicted in Roger Seymour's work (going back as far as 1976, so we're well aware of it!) Sorry if that sounds evasive: hopefully we'll have a more convincing response for you within a year or so.

4. Finally, we want to be clear that we don't think our paper ends the debate. If anything, it re-opens it, as horizontal-to-dropping sauropod necks have been orthodox for the last decade or so. There's more work to do (but we're on the case!)

That's all for now -- hope it helps. If you have any more questions, you're welcome to ask, and we'll do our best to answer. The best place to do is probably over on Sauropod Vertebra Picture of the Week, as I and my co-authors each check that several times a day. http://svpow.wordpress.com/

more than 5 years ago
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Free Global Virtual Scientific Library

Mirk Re:Shouldn't it already be this way? (113 comments)

Has the issue ever run its full course, human rights battling the law?

I don't know. That would be interesting: an author having sold his copyright to a publisher, then asserting his human right to the copyright anyway. I've not heard of such a case, and I have no idea how it would turn out. My money would be on the publisher, though :-P

more than 7 years ago

Submissions

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PeerJ is changing everything in academic publishing

Mirk Mirk writes  |  about a year and a half ago

Mirk writes "Academic researchers want to make their papers open access for the world to read. If they use traditional publishers like Elsevier, Springer or Taylor & Francis, they'll be charged $3000 to bring their work out from behind the paywall. But PeerJ, a new megajournal launched today and funded by Tim O'Reilly, publishes open access articles for $99. That's not done by cutting corners: the editorial process is thorough, and they use rigorous peer-review. The cost savings come from running lean and mean on a born-digital system. The initial batch of 30 papers includes one on a Penn and Teller trick and one on the long necks of dinosaurs."
Link to Original Source
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Petition Obama to mandate free access to research

Mirk Mirk writes  |  about 2 years ago

Mirk writes "The UK and the European Union are both in the process of introducing mandates that all publicly funded research must be publicly accessible. At the moment, the USA has no concrete plans to do the same. But Open Access advocates have the ear of Obama's scientific advisor and think there's a good chance this could change — PROVIDED that citizens show it's an issue we care about. So please sign the Whitehouse.org petition at http://wh.gov/6TH"
Link to Original Source
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Doctor Who: what's in the Pandorica? (No spoilers)

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "Season Five of Doctor Who — the first season to feature Matt Smith as the Eleventh Doctor — is drawing to a close. Only the final two-part story remains to be shown, consisting of The Pandorica Opens and The Big Bang. But what is inside the Pandorica? With only a few days left before the episode is broadcast, The Reinvigorated Programmer speculates, on the possibilities."
Link to Original Source
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The 11th Doctor hits his stride (The Beast Below)

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "Matt Smith, the 11th actor to take the eponymous lead role in Doctor Who, got off to a rocky start in his first episode, The Eleventh Hour. In his second outing, The Beast Below, Smith is starting to emerge from the long shadow cast by his predecessor David Tennant. This review looks at how the second episode the new series exemplifies all the things we have come to love about Doctor Who."
Link to Original Source
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Doctor Who: first impressions of the 11th Doctor

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "The first episode of Doctor Who's new series 5 has just aired on BBC1 in the UK. This is an important episode for the show because so much has changed: Matt Smith plays the new Doctor, replacing David Tennant, and Karen Gillan portrays a new companion, Amy Pond. Maybe most important, Russell T. Davies is replaced as showrunner by Stephen Moffat, who's known for acclaimed Doctor Who scripts including The Empty Child and Blink. The Reinvigorated Programmer offers an early review of the new Doctor, companion, showrunner, and series."
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"Simplicity" in programming: two opposing views

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "Every good programmer agrees on the need for simplicity, clarity and generality. But those are abstract qualities, and it's never been established what concrete properties of code make it simple to read, understand and modify. Books like Fowler's Refactoring advocate decomposition into many small classes, each with many tiny methods, but that approach brings problems of its own. Might it be better to retain fewer, larger methods? Or could it be that different people with different aptitudes prefer different approaches?

Discussion at Hacker News [http://news.ycombinator.com/item?id=1224071] has been very provocative, and the author has responded with a followup [http://reprog.wordpress.com/2010/03/28/what-is-simplicity-in-programming-redux/]"

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Hacker, architect and superhero: three programmers

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "We all know programmers whose skills humble us, but software skills don't just fall on a linear scale of worst to best: good programming comes in many different and sometime incompatible flavors. This article looks at three individuals who excel in very different ways, and asks what the rest of us can learn from them. Which one are you?"
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Trying to "Say what you mean, simply and directly"

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "One of the first rules in Kerninghan and Pike's classic The Elements of Programming Style is "say what you mean, simply and directly", and this is one of the most universally applicable of all programming guidelines. The Reinvigorated Programmer argues that structure-rich languages like Java and C++ simply don't allow you to do this, that the scaffolding obscures the actual building, and that higher level languages such as Ruby allow code to be much shorter and more comprehensible."
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Programming the Commodore 64: The Definitive Guide

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "Back in 1985 it was possible to understand the whole computer, from the hardware up through device drivers and the kernel through to the high-level language that came burned into the ROMs (even if it was only Microsoft BASIC). The Reinvigorated Programmer revisits R. C. West's classic and exhaustive book Programming the Commodore 64 and laments the decline of that sort of comprehensive Deep Knowing."
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A different take on functional programming

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "An imperative program tells you how to calculate a factorial, whereas a functional program just says what a factorial is. The Reinvigorated Programmer tries to get to grips with the alien world of functional programming, and wonders whether the real question is which approach scales better to realistic-sized problems?"
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The value of BASIC as a first programming language

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "Computer-science legend Edsger W. Dijkstra famously wrote: "It is practically impossible to teach good programming to students that have had a prior exposure to BASIC: as potential programmers they are mentally mutilated beyond hope of regeneration". The Reinvigorated Programmer argues that the world is full of excellent programmers who cut their teeth on BASIC, and suggests it could even be BECAUSE they started out with BASIC."
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Whatever happened to programming?

Mirk Mirk writes  |  more than 4 years ago

Mirk writes "In a recent interview, Don Knuth wrote: "the way a lot of programming goes today isn't any fun because it's just plugging in magic incantations — combine somebody else's software and start it up." The Reinvigorated Programmer laments how much of our "programming" time is spent pasting not-quite-compatible libraries together and patching around the edges."
Link to Original Source

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