Making packages is a great way to organize R code, whether it’s a set of scripts for personal use, a set of functions for internal company use or a lab group, or to distribute your new cool framework foobar to the masses. There’s a number of guides to writing packages, including http://r-pkgs.had.co.nz/. As you develop packages there’s a number of issues that don’t often get much air time. I’ll cover some of them here.

I was talking to a speaker visiting our department recently. While discussing his postdoc work from years ago, he told me about the identification of the sperm factor that causes calcium oscillations in the egg at fertilisation. It was an interesting tale because the group who eventually identified the factor – now widely accepted as PLCzeta – had earlier misidentified the factor, naming it oscillin.

Titktaalik roseae. Image from https://tiktaalik.uchicago.edu/index.html The second post in my series on limb evolution is now up at the BioLogos site. This installment reviews the fossil evidence on fin-to-limb evolution, introducing the famous Tiktaalik . Next up: evidence from developmental biology. The first post at BioLogos outlined limb structure and some historical background.

Last month, I started a series on the topic of limb evolution, here at Quintessence of Dust. That series has been transformed (through a series of intermediates) into a series of posts* at the BioLogos site. The first installment is now up, and it provides an expanded introduction to the topic and a little historical context.

The discovery of deep homology was a milestone in the history of evolutionary thought. Anatomical structures in distantly related organisms, structures with only the barest of functional similarities, were found to be constructed under the influence of remarkably similar genetic pathways. The original and classic example from 1989 involves genes controlling pattern in both insects and mammals – the famous Hox genes.

"The Selfish Gene." "Selfish DNA." Oh, how such phrases can get people bent out of shape.  Stephen Jay Gould hated such talk (see a little book called The Panda's Thumb ), and Richard Dawkins devoted more time to answering critics of his use of the term 'selfish' than should have been necessary.

Given that disputes over the existence and meaning of the phylotypic stage and the hourglass model have simmered in various forms for a century and a half, the remarkable correspondence between the hourglass model and gene expression divergence discovered by Kalinka and Varga and colleagues would be big news all by itself. But amazingly, that issue of Nature included two distinct reports on the underpinnings of the phylotypic stage.

The controversy about the existence of the phylotypic stage is more than some bickering about whether one blobby, slimy fish-thing looks more like a Roswell alien than another one does. It's about whether the phylotypic stage means something, whether it tells us something important about development and how developmental changes contribute to evolution.

Disputes and controversies in science are always a good thing. They're fun to read about (and to write about), and they're bellwethers of the health of the enterprise. Moreover, they tend to stimulate thought and experimentation. Whether scientists are bickering about evo-devo, or about stem cells in cancer, or about prebiotic chemistry, and whether or not the climate is genial or hostile, the result is valuable.

Last month, PZ Myers wrote an interesting piece at the Panda's Thumb in which he discussed some problems with very simple models of evolutionary genetics. One of his main themes was the idea that many genetic changes are neutral with regard to fitness;