Now Blogging at movingthelamppost.com

Hello anyone who might be following this still.  I will now be blogging from http://movingthelamppost.com

I have recently joined the trend of taking my blog ‘static’ rather than using a more complicated database driven solution like WordPress. One major reason for me is that I like to write content in abstraction. I love LaTeX for this reason and I love Sphinx for the same reason. I chose Tinkerer as my static engine because it is actually built from Sphinx and it is written in my favorite language (Python). Sphinx is a code documentation framework originally built for python. I use it to generate my documentation using reStructuredText markup. I figured since I am more-or-less used to the way Sphinx does its markup, I would choose a blog engine that worked the same way. So far, I like it. It is a bit less mature than some of the other static engines out there (Octopress being a VERY popular one) but I think it will grow nicely.

My main goal for Moving The Lamppost is to serve as a place for me to record random thoughts about my work and what is going on in science at large in such a way that I can engage in dialog with others about it. Relating to that goal is my desire to foster relationships with other scientists or informed hobbyists that can approach what is termed Open Science. I hope to make this my home base for sharing what I am interested in as well as what I am actually working on: including data and figures.

Hope to engage you there!

Gus

The Thesis Whisperer’s thoughts on “The academic writer’s strike” and Elsevier

So I just caught wind of this blog but from the first few posts I glanced through, it seems a gem. This one raises some good questions regarding the academic publishing cycle and whether it is fair or actually achieves the goal of supporting the ideals of the academic endeavor: clear, accurate, and far-reaching dissemination of original ideas for the purpose of helping other people come up with original ideas to disseminate.

I think that in many ways the open publishing movement (BMC, PLoS, and similar) goes a good way to helping the problems that she raises but you cant beat the impact factors of many of the “old school” publication companies. I am interested to continue reading Mewburn’s material and suggest that you check her out as well.

The Thesis Whisperer

I have spent years exhorting students to publish as much as possible before they finish and straight after. But lately I am beginning to wonder about my place in the academic publishing system, both as a researcher and a teacher.

I don’t think I can keep handing out this advice with a clear conscience.

Academic publishing is presented as a universal good, without regard to how the publishing system operates. While publications are an essential addition to the CV in today’s competitive job market, the ethics of publishing need to be considered too. Some big publishers are making boatloads of money – in the order of millions of dollars – out of labour we academics willingly give them.

This profit largely goes into the pockets of shareholders, not the researchers or universities.

Essentially this is public money which becomes ‘privatized’. It works a bit like this. Australian citizens are…

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Google is still better than most of Corporate America

Google STILL Rocks

This is one of the reasons that Google is STILL way better than LOADS of other companies.

Google is continuing one of the coolest ideas I have ever heard of!  Last year Google launched:

the first ever global online science competition for 13-18 year old students with the Google Science Fair. Over 10,000 students from 91 countries submitted amazing science experiments. With project topics ranging from “Can I program a robot in English?” to “Can I make a sailboat even faster with a winged keel,” to “How does marinade affect carcinogen levels in grilled chicken?”…

Not only that, they seem to be doing a damn good job of including one the smartest demographics our species has to offer, THE LADIES!

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Evolution and gravity: theory? fact? law? Or: Why Ron Paul and other politicians must stop crying ‘theory’!

Background and Significance:

Recently, a pretty old YouTube clip of Ron Paul explaining that he does not accept the “theory of evolution” showed up in my Facebook feed.   It was posted by the Secular Student Alliance and provoked quite a bit of debate in the comments.  The video is from late 2007 and the relevant question posed to Paul was regarding whether or not he had raised his hand on May 3rd, 2007 when the Republican candidates at a televised debate were asked to do so if they did NOT believe in evolution.  Only three candidates raised their hands; Ron Paul was NOT one of them, by the way.

However, in this video clip, set in a more conservative, Christian setting, he affirms that:

“Well, first I thought it was a very inappropriate question, you know, for the presidency to be decided on a scientific matter… and uh, I think it’s a theory…the theory of evolution and I don’t accept it as a theory. But it really doesn’t bother me… Its not the most important issue for me… to make the difference in my life to understand the exact origin.  I think the creator that I know, you know… created us, every one of us and created the universe and the precise time and manner… and all. I just don’t think we’re at the point where anybody has absolute proof on either side.” … “I think its a theological discussion and we can have our… but if that were the issue of the day, I wouldn’t be running for public office! [laughter]”

Now there are a LOT of things we could talk about in this one clip — like whether or not the leader of the most scientifically and technologically advanced nation in the world (which btw depends on “scientific matters” to produce the vast majority of its GDP) should reasonably be expected to demonstrate a basic understanding of rudimentary scientific topics; or the old, tried-and-true trick of claiming that this is a theological question that allows for multiple opinions and points-of-view — but I want to focus this post specifically on the miss-use of the word “theory” that Paul and almost every politician today commits on a regular basis.

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siniXster’s cloaked spaceship hypothesis

Said the tin-foil-hat-wearing,  little-grey-men otaku () of the coronal mass ejection (CME) as it passed Mercury and “seemed” to illuminate a near by object:

“It’s cylindrical on either side and has a shape in the middle. It definitely looks like a ship to me, and very obviously, it’s cloaked…”

  • Before I continue: for a much less snarky response to this (and certainly higher quality) this article goes into a bit more of the specifics as explained by the researchers themselves.

So when the folks who actually analyze this stuff are asked (imagine that revolutionary idea), it turns out that these images are MASSIVELY “manipulated” using “tricks” (as in ‘hide the decline’ kind of tricks [look it up]) to create an effective graphical representation.

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Simple Sliding Window Iterator in Python

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A common task encountered in bioinformatics is the need to process a sequence bit-by-bit, sometimes with overlapping regions.  I have provided an example of a very simple; easy to extend; and stand-alone python iterator that returns a single defined window of any python string object per iteration to allow simple, intuitive handling of sliding window tasks.  The code is simple to understand, and does not depend on other packages.

Consider the task of scanning a sequence of length l for a pattern representing a transcription factor binding site (TFBS) or other feature-of-interest.  You must start at the first position in the sequence (i = 1), retrieve a chunk of the a specific length (k) and test it for the probability that it embodies the feature’s described qualities.  You must then return to the original sequence and retrieve a chunk of length k with a position off-set of one DNA letter forward into the sequence (i = 2).  This process is repeated until the last chunk of length k is encountered at position i = lk.

This type of process is called a sliding window.  For example, consider the sequence “ATCGATGCTA”.  It has an l of 10.  If the feature that we are interested in has been described to usually be 5 bp long, we would define our k (window size) to be 5.  Our step size (how far to advance the chunk’s starting position each time) will generally be 1 for this type of problem, but one might conceive reasons to use larger step sizes for different purposes.  I have diagrammed the result of the sliding window procedure for our hypothetical sequence below. Continue reading

SciPlore: Mind-mapping for academic writing

As a Ph.D. student, I am constantly trying to improve my ability to communicate the findings of our lab and my work to others.  A central part of this effort in any academic setting is the composition and publishing of scholarly articles and presentations.  One of the keys to a great paper or presentation (other than actually having something interesting to talk about) is organization and flow.  If the end product is a paper, you will also need to maintain and easily refer to dozens and sometimes hundreds of citations to past papers that relate to your work.

An international group of scientists and software engineers have adapted the existing mind mapping software called FreeMind to make it a bit more targeted to planning and writing academic communications.  Probably the biggest improvement they have made to FreeMind with a mind to academics is the ability to effortlessly integrate your entire library of PDFs and references into SciPlore.

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