Installing Gerd Neu­ge­bauer’s Bibtool on OS X

9 April 2014 § Leave a Comment

I struggled for more hours than I would like to say trying to compile Gerd Neugebauer’s BibTool utility on my mac (OS 10.9.2). I kept running into problems with the kpathsea libraries. Not surprisingly, an old thread on the Mac OS-TeX mailing list provided the necessary insight. I’m reposting it here so that it might get better exposure on the Internet for those trying to do the same thing. Of course, someone who wasn’t shamelessly hacking away at it probably wouldn’t have had any problem at all . . .

BibTool is an amazing utility that does all those things we all wished BibDesk would do, but doesn’t: command line tools for removing fields, rewriting fields, grabbing references based on various criteria including regular expressions, pretty printing.

On Nov 23, 2009, at 1:49 PM, Jan Erik Moström wrote:

> I’m a bit slow (in all kind of ways ;) and I’m just trying to figure out the MacTeX distribution … one thing that that I would like to do is to install “bibtool” (not bibtools) but I can’t figure out how to do this in a simple way. Using Gerbens TeX distribution it was possible to use the i-installer but now I’m at a loss how to do it.

You can download the source and compile it yourself from
(Get the *.gz) file.
Once you have expanded the tar archive, copy the makefile.unx file to makefile, then run
sudo make install
sudo make
This will place a working copy and manual pages in the /usr/local tree.
As long as you have /usr/local/bin in your path, things should work.

Of course, you have to have the developer tools to do this.
There are many options to set specific details during the compilation process, but I just did a vanilla “make” and
./bibtool -h
gave me the typical “usage” statement.

I’ve never used bibtool, don’t know how to use it, and don’t have any test files to ensure that it works in a real-life situation.
Otherwise, I now have a seemingly-functional version of “bibtool” that runs on X86_64 Snow Leopard.
I don’t guess that really helps you, but if you want it, send me a message off-list.

Believer micro-interview on the March

10 March 2014 § Leave a Comment

At the end of last summer, Nicholas Hune-Brown interviewed me over the phone. I answered his questions—it was more like a discussion really—about the march of progress, as I paced more and more rapidly from one end of the invertebrate paleontology lab at the AMNH to the other end. Nicholas distilled our conversation to its essence, which has been published in the form of a Believer micro-interview. Like so much that’s worth reading, the full interview is protected by a pay wall. A subscription to The Believer costs about as much as buying a single article from Springer or Elsevier, and this is independent journalism, which is well worth supporting. You can read it online, but you’ll want to have the print edition too.

I’m posting this now because I was so nervous about how it would come out that I put off reading it until now.

If anyone thinks I am making too big a deal over the March of Progress image, well, go ahead, because almost everyone gets to think what he or she wants to, which does not, of course, make it right.

March of progress, reloaded

5 March 2014 § Leave a Comment

To compensate for the um, excitement of that last post about project management, I present my readers with this especially striking depiction of the March of Progress image.


[March of Progress image]

There are two central points about this image, generally speaking. First, it represents evolution incorrectly. The figures become more upright towards the right side of the image, which is intended to represent progress towards modern-day human beings. Evolution does not progress, let alone towards us. Second, it’s racist. Portrayals of dark-skinned people as primitive had been a staple of racists since well before the late 1850′s; evolutionary biology simply provides a new context for this representation. It remains offensive; those who think it isn’t aren’t taking it seriously enough. Recall the 2009 controversy over the representation of Barack Obama as a monkey—being shot by police. The Tightrope web site (“It’s not illegal to be white. . . yet”) has a t-shirt using a monkey to represent Obama, and if you really think this isn’t racist, you can show the world by buying one. I point out the scientific problems first to pre-empt the inevitable knee-jerk criticism that political correctness is the motivation for my complaints about the image. Even Grand Wizards and Neo-Nazis should object to this image on scientific grounds, although I doubt that the ignorance and intolerance framing their world view does not promote serious study of evolutionary biology.

This instance is especially outrageous because the March of Progress is a march towards whiteness. Astonishing. It’s not my area of expertise, but is it correct that the 4th and 5th figures from the left have hairstyles more likely to be worn by people of African descent? The rightmost woman has hair not in general natural for a person with black skin, because it is brown.