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PLoS-1 published a “creationist” paper: some thoughts on what followed

As everyone knows by now, PloS-1 published what seemed to be a creationist paper. While references to the ‘Creator’ were few, the wording of the paper strongly supported intelligent design in human hand development. A later statement from the first author seemed to eschew actual creationism, but maintained teleological (if not theological) view of evolution, […]

Why scripting is not as simple as… scripting

If you haven’t read the transcript of Sean Eddy‘s recent talk “On High Throughput Sequencing for Neuroscience“, go ahead and read it. It’s full of many observations and insights into the relationships between computational and “wet” biology, and it is very well-written. I agree with many of his points, for example, that sequencing is not […]

Announcement: WikiProject Computational Biology Competition

WikiProject Computational Biology/ISCB competition announcement 2013 The International Society for Computational Biology (ISCB) announces an international competition to improve the coverage on Wikipedia of any aspect of computational biology. A key component of the ISCB’s mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at […]

Are you using this blog for teaching, studies or writing?

Dear readers (Yeah, I’m talking to both of you!) If you are a school teacher, college professor or any kind of other educator, trainer or science writer, and if you have ever used this blog in your line of work, please let me know. Also, if you are a student and used this blog as […]

Adding supplementary tables and figures in LaTeX

A problem I encountered now, when revising a paper and adding a supplement per the editor’s request. How do I number my tables and figures as Table S1, S2 etc.? A solution was provided in Stackexchange, but the syntax was not good for my version of LaTeX, and I don’t like \makeatletter (here’s why). Here […]

Group review of papers?

So I’ve been catching up on my paper reviewing duties this weekend. To those outside the Ivory Outhouse, “reviewing a paper” means “anonymously criticizing a research article considered for publication in a scientific journal”. (For those of you familiar with the process, you can jump to the text after the first figure.) Here’s how science […]

Wool / Omnibus: Make your Choice

I finished reading Wool / Omnibus a few days ago. If you want one captivating book (or rather pentalogy) to read by the end of the year, then this is it. The five books  grew from a short story, Wool, published electronically. The author, Hugh Howey, continued to publish Wool 2-5, and then compiled all […]

Open Access Explained. Well.

Today is the last day of Open Access Week, where all things Open Access are heralded. William Gunn gave a great talk here at MU on how open access is changing scholarship. (And a big thank you to our librarians Jen Waller & Kevin Messner for hosting William!)  I have posted about Open Access before, […]

DNA half life, and my dream of an Allosaurus Army

Let’s get this clear: Tyrannosaurus rex, the best selling figurine of class reptilia is not my favorite bad-ass top-of-the-food chain predator. Come on. Did you see its arms? I mean…   As a kid, I always thought the Allosaurus was much cooler. For one thing, it was on the cover of my favorite dinosaur book, “The […]

Taming the Impact Factor

Quite a bit has been written about how the journal impact factor (JIF) is a bad metric. The JIF is supposed to measure a journal’s impact using a formula that normalizes the number of cited articles in  a given time frame (typically a year). It is calculated exclusively by Thomson-Reuters, and is trademarked by this […]

Repost: the Scope(s) of Substance

This tweet from Neil Degrasse Tyson jolted me from a pleasant rest before tomorrow’s race:   …which led to the (in)famous Scopes Trial. On May 5, 1925 John Scopes was charged and subsequently tried, found guilty, and fined $100 for teaching Evolution, a violation of Tennessee’s Butler Act. The trial became a battleground for science […]

And I should go because?

Found this in my inbox: Dear Dr.Iddo Friedberg,     Greeting from OMICS Group! I came across your contribution entitled “Biopython: freely available Python tools for computational molecular biology and bioinformatics” published in the Journal of Bioinformatics and thought your expertise would be an excellent fit for Toxicology-2012 Conference that OMICS Group is hosting.   I’m just wondering how many legitimate calls for […]

Biocuration 2012

  Great meeting:  Biocuration 2012, Georgetown University, DC.  When I leave a meeting with my head exploding with new ideas and a need to try them all out at once, I know I got my money’s worth, and then some. Even a three hour flight delay followed by discovering my car with a dead battery […]

Wikipedia pages on protein function prediction

I just received an email from Julian Gough , one of last year’s CAFA participants. He started a Wikipedia initiative on protein function prediction, which are barely stubs at the moment. EDIT: He alerted me to the fact that protein function prediction has virtually no presence on Wikipedia. So all you protein function predictors out there, please contribute. Yes, […]

Oh, but to receive such a rejection letter!

It is with no inconsiderable degree of reluctance that I decline the offer of any Paper from you. I think, however, you will upon reconsideration of the subject be of opinion that I have no other alternative. The subjects you propose for a series of Mathematical and Metaphysical Essays are so very profound, that there […]