moving the blogs

so any and all blogs i do are going to blogspot. nothing new going here and it will come down soon.

see you there

science – http://semaphoront.blogspot.com/

code — http://codeink.blogspot.com/

I’m back

I was pretty busy because I was writing up the PhD, but I am back now. We will try again to be better about keeping things up to date.

phylogenetics comes of (numeric methods) age

So I just picked up Numerical Recipes 3rd edition.

For those of you that don’t know this book, it is a standard for algorithms and code examples for any number of (as the title suggests) numerical methods. The last edition was in 1992 (for C++ that is, however the language doesn’t really matter does it–they can all be ported–and should be considering the license won’t let you copy).

Now the important part. One of the major updates includes PHYLOGENETIC TREES! Pretty exciting that scientific computational people have decided to include phylogenies. On their own as well. They didn’t add an author that is into phylogenies, just an addition.

Way to go.

Richard Stallman: attacked by ninjas at Yale

For those of you that don’t know, Richard Stallman is the GNU guy. He helped author much of the software, ideas and other things for the Free Software movement and GNU movement. (Also…emacs — your other OS).

Anyway, he was at Yale on Wednesday at the Union debating on DRM’s illegality. I believe he won as well, convincing people that it should be illegal — a first for the Union — going against current public or business opinion.

Before he got on stage however,  he was attacked…

Here is the comic they were reenacting. Here are some links to better accounts — one — two

two great mac packages (from a linux user)

So I  am not usually a mac advocate. I don’t like the lock ins, I don’t like the culture, and I don’t like that Apple thinks they know what I loke or need more than I do. Most of the time they don’t. It is a fact of phylogenetic life however, that I have to use a mac. Therefore, I often look for mac versions of linux staples.

Well today, I found some great ones. Here are the links: Aquamacs which is a mac package of emacs. Now I know that emacs is available by default if you just type emacs in the terminal but this one is different. It is like what the x emacs is striving for and it is done for the mac first. Pretty great. Comes with all the add-ons (color themes, programming laguage support, etc).

The other, MacTeX, is the texlive package for mac and again with all the addons, especially if you download the extras package too. This makes a normal LaTeX environment a reality for the mac platform.

Pretty great. Now I am slightly less annoyed by the mac standard in phylogenetics.

rates of language evolution (with some phylo people)

A great paper in Nature  on the Frequency of word-use predicts rates of lexical evolution throughout Indo-European history by Mark Pagel & Quentin D. Atkinson & Andrew Meade was published. It is a pretty great study of rates of evolution on a small scale (time wise).

How do others see Biological efforts?

A recent post on Bleeding Edge BioTech about Mathematics vs. Physics vs. Biology brings up an interesting issue with how other scientists see community efforts in biology. Here are the images that summarize the post:

Basically there may be the perception that  biologists efforts are mostly not community wide. I wonder whether this is just a problem on the definition of problem. Perhaps the figure about biologists describes biologists approach to smaller problems?

Books as Software or avoiding traditional publishers

Should authors or potential authors be discouraged to write books without a contract?
Shriram Krishnamurthi, author of Programming Languages: Application and Interpretation, has an article explaining the pros and cons of avoiding traditional publication routes. In other words, why would someone release there book online without a traditional publisher.

This isn’t something like Wiki-Books or anything, these are actual books that are of the quality of traditionally published books, but for whatever reason that route is avoided.

Sounds like a great idea for the sciences considering how frequently our methods, results and evidence are updated.

The only things to overcome are permanence and the ego aspects of having a published book in print. We can get over those I think.

Just for your info, here is another book,  How to Design Programs.

More comics?

Yep, in some random interweb searching, I stumbled across a comic version of 1984 (well the first two chapters). It is more lengthy than Crime and Punishment and DOESN’T include Mickey Mouse as Winston Smith or anything of the sort. It’s worth a look. Not sure about the cover art (looks like Hitler, when I think Oceania is more like a future dystopia along the lines of the Soviet Union, and Wikipedia agrees so who can argue with that).

Dostoyevsky and Batman?

That is right. Apparently there is a Batman version of Crime and Punishment. Good or not it is worth checking out, and I am sure you were picturing Raskolnikov as Batman when you read it anyway.