The Futile Cycle

I just saw this in PLoS Computational Biology:
Matt: Local Flexibility Aids Protein Multiple Structure Alignment.

I thought to myself, Matt? What’s that?

Technically, it stands for “Multiple Alignment with Translations and Twists.” But really, “Matt” is just an algorithm named after the first author, Matthew Menke.

Cute or egotistical, what do you think?

For all of you geneticists out there, here’s a nice quip from David Botstein, a yeast and former bacterial geneticist:

In Microsoft Word’s “Track Changes” and Endnote are synthetic lethals.

For the non-geneticists, a synthetic lethal pair of genes are two gene variants that alone are fine, but when combined into the same organism, cause it to die.

Happy Holidays to all of you. And to those of you still in lab over the holidays, cool (and gross) seasonal Petri dish art! (h/t Miya)

It’s common sense, but strangely a lot of people don’t seem to get this:

“Linux is only free if your time has no value.” — Jamie Zawinski

From The Introduction to Software Carpentry.

One of the topics that came up at a “town hall” meeting between graduate students and the department faculty recently was how to increase attendance of the department seminars. There were some good insights, like “attendance at each seminar is inversely proportional to the frequency of seminars”, but really, was it that hard to miss the most compelling incentive to attend seminars? It seemed like 50 scientists just could not figure out!

Today’s Ph.D. comic summarizes:

One person spoke up and mentioned, in passing, “It always seems like more people come if you put out snacks.” The comment was mostly ignored, in favor of other speculation, like “what if you send out abstracts of the relevant papers beforehand?”

Hellooo! Feed them, they will come!

Science has a reputation for really esoteric jargon, but sometimes science writing is refreshingly casual (Liu, XS (2007) PLoS Comput Biol 3(10): e183):

“If users encounter array images with blob defects, they are advised to use a ‘microarray blob remover’ to detect and remove affected probes before running MAT.”

Ah yes, the hi-tech “blob remover” algorithm.

Scientific Misconduct Blog has an excellent graph from the literature, and a wonderful rebuttal. Alas, I doubt such things would be published in this too-serious era.

One of the amusing things to look at when I have time in between experiments is to look at what kind of search phrases people use to find the site. The best ones are from the long tail of search phrases that only one person would ever type:

“earthworm hammer dissection”. I don’t know about you, but generally I don’t use hammers when dissecting things as small as earthworms…

“vitameatavegamin medicine”. I don’t really want to know how many people are taking medical advice from “I Love Lucy”.

“is well done steak higher in water than rare”. I’m not really sure what this means. Are they asking whether well done steak has more water? (It doesn’t.) Are they asking whether it floats compared to rare? (I have no idea.)

“how in the hell does a person create a ‘table of contents’ in microsoft word 2007″. Someone is really frustrated! I don’t know. I’ve sworn off using Word unless I absolutely have to.

“should we treat hospitals differently than we treat farms, car”. There are lots of things wrong with the current health system, but that doesn’t mean we should take it out to the pasture. (cricket) Is this asking about subsidies? I hope we treat our hospitals differently from cars…

“when i hear biochemistry, i think of”. Well, I think of lots of pipetting. And blots. Lots of blots, lots of buffer. And sometimes some nifty, but really expensive, machines.

“what is a parafilm in chemistry?” I’m a big fan of parafilm. It’s a form of wax in a sheet, with some additives that make it more elastic. It’s like the sophisticated man’s plastic wrap, the scientist’s duct tape. More praises cannot be poured over parafilm.

I’ve kept this back for a long time, but sometimes I just can’t help myself to a bad pun or two (or three), so here it is, the world’s worst biology/programming combo joke. Please, look away, it isn’t pretty. (Prerequisites: Perl, some knowledge of biology)

So, what is this Perl subroutine?

sub p53
{
  my @n_mer = @_;
  if (scalar(@n_mer) == 2) {
    return ();
  }
  return @n_mer;
}

It’s a “two-mer” suppressor!

I warned you.

From S. Sarkar (1991), Genetics, 127, 257-261. (PDF):

“[The talk on the "Statistical Theory of Bacterial Mutations"] was attended, Delbruck (1946) observed, ‘by those who took the phage course this year and by a few outsiders, mostly people to whom algebra is more strange than Chinese.’”

It seems the paucity of mathematical prowess in biology was evident even back then.