I've recently been resurrecting some comparative genomics methods I developed in my last year of grad school, but never got to publish. These build on previous work to locate what we called Synonymous Constraint Elements (SCEs) in the human genome: short stretches within protein-coding ORFs that also encode additional, overlapping functional elements - evidenced by a markedly reduced apparent rate of synonymous substitutions in cross-species alignments. The first step in this analysis, and the subject of this post, involves extracting the cross-species sequence alignments of protein-coding ORFs from raw, whole-genome alignments. I hope to write a series of blog posts as I get various other parts of the pipeline going. I'm not exactly sure where it'll go from there, but it's pretty neat stuff I would eventually like to get peer-reviewed!
Thursday, May 23, 2013
Sunday, May 19, 2013
Testing MathJax on Blogger
$$
\hat{\mathcal{H}} = \frac{4 N_e u}{1+4 N_e u}
$$
Followed these instructions, except the place where you can edit the HTML in the Blogger dashboard has moved: it's now under the "Template" tab, then the "Edit HTML" button.
\hat{\mathcal{H}} = \frac{4 N_e u}{1+4 N_e u}
$$
Followed these instructions, except the place where you can edit the HTML in the Blogger dashboard has moved: it's now under the "Template" tab, then the "Edit HTML" button.
Saturday, May 4, 2013
Lamenting the rise of the bio-brogrammers
A couple years ago the "brogramming" meme spread through Silicon Valley and the broader tech world. One manifestation would feature a hipster-filtered photo of the eponymous brogrammer in Wayfarer sunglasses, popped collar, drink or dumbbell in hand, tapping on his laptop in some incongruous setting. A former colleague of mine featured herself in some of the funniest ones I can remember. Less-tasteful versions included scantily clad women in supporting roles.
The meme started innocently enough, of course: as an expression that the ranks of software engineers aren't just populated by pale, odorous introverts with their glasses held together by tape. But then we thought about the meme and the attitudes that underlie it.
Today, it's de rigueur for tech companies to openly denounce brogramming and its sexist, exclusionary undertones. Not only because it's the right thing to do, but it's also a matter of survival: it's simply too hard to find top talent, and we cannot risk alienating wide swaths of the pool. The fall of brogramming was, of course, just one step in an ongoing journey, which continues to hit roadbumps.
Over the last few days, we saw echoes of this attitude in the genomics and bioinformatics community, when a twitter meme erupted featuring maternal insults phrased in terms of genome size. Most of these were hilarious and innocent. Some were clever but also sexist and degrading - conflating C-value with bra cups, giggling at those TATAs, or interpreting the .bed and .bam file formats as verbs, to call out some unfortunate examples. A few were just horrible.
The meme started innocently enough, of course: as an expression that the ranks of software engineers aren't just populated by pale, odorous introverts with their glasses held together by tape. But then we thought about the meme and the attitudes that underlie it.
Today, it's de rigueur for tech companies to openly denounce brogramming and its sexist, exclusionary undertones. Not only because it's the right thing to do, but it's also a matter of survival: it's simply too hard to find top talent, and we cannot risk alienating wide swaths of the pool. The fall of brogramming was, of course, just one step in an ongoing journey, which continues to hit roadbumps.
~~~
Over the last few days, we saw echoes of this attitude in the genomics and bioinformatics community, when a twitter meme erupted featuring maternal insults phrased in terms of genome size. Most of these were hilarious and innocent. Some were clever but also sexist and degrading - conflating C-value with bra cups, giggling at those TATAs, or interpreting the .bed and .bam file formats as verbs, to call out some unfortunate examples. A few were just horrible.
Thursday, May 2, 2013
Bagram 747 crash video & speculation
An incredible, horrifying video has emerged apparently of the 747 cargo plane crash at Bagram Air Force Base in Afghanistan this past Monday.
Early speculation (and it is speculation) has focused on a shift of the cargo inside the plane, which was reportedly carrying several military vehicles. How could some cargo shifting around possibly cause such an utter catastrophe?
Consider this simple model of how an airplane stays under longitudinal (pitch) control:
Early speculation (and it is speculation) has focused on a shift of the cargo inside the plane, which was reportedly carrying several military vehicles. How could some cargo shifting around possibly cause such an utter catastrophe?
Consider this simple model of how an airplane stays under longitudinal (pitch) control:
Sunday, March 3, 2013
Why the natural sciences rely on affirming the consequent (and that's OK!)
Last weekend, I discussed a paper by Graur et al., which (among many other criticisms and insults) accused the ENCODE consortium of basing certain interpretations on a fallacy in deductive logic called "affirming the consequent." I pointed out how bizarre that criticism was, because "affirming the consequent" is actually a necessary and justified part of reasoning in the natural sciences.
Many readers seemed to be surprised by and skeptical of this claim, and some probably thought it proof of my insanity. I must, first and foremost, once again beg such skeptics to read Jaynes' outstanding book. The first few chapters are actually available as a free pdf, but the whole book is really worthwhile. If you're an academic, you can probably find the book in your library system.
Understanding, however, that the urging of an apparent madman may not be adequate motivation, I thought I'd try to explain a bit more why this is, actually, the case.
Many readers seemed to be surprised by and skeptical of this claim, and some probably thought it proof of my insanity. I must, first and foremost, once again beg such skeptics to read Jaynes' outstanding book. The first few chapters are actually available as a free pdf, but the whole book is really worthwhile. If you're an academic, you can probably find the book in your library system.
Understanding, however, that the urging of an apparent madman may not be adequate motivation, I thought I'd try to explain a bit more why this is, actually, the case.
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