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.

Review: The Bloodless Revolution: A Cultural History of Vegetarianism from 1600 to Modern Times

The Bloodless Revolution: A Cultural History of Vegetarianism from 1600 to Modern Times by Tristram Stuart amazon

Let me first state that I like non-fiction most. Not any particular genre of non-fiction, just non-fiction. I dabble in fiction from time to time, but can always read a good history, philosophy, or, of course, science book.

This book is right up my alley (whatever that means). Basically, it reviews the history of vegetarianism (in Europe) from 1600 to 1800 and then has an epilogue where it discusses from 1800 to 1940’s.

One very important message I took away from this book is that modern vegetarians are not alone and are generally not unique. This is a similar conclusion when reading many books on Atheism (such as The God Delusion). The arguments used by vegetarians today have basically all been argued before in some capacity.

It also brings up an important point that I have noticed subtlety while being a member of the scientific (more specifically, biological scientific) community. Basically, there seems to be a general lack of respect for vegetarianism (with some exceptions). However, what you learn from a book like The Bloodless Revolution is that vegetarians are generally in good company (excluding all those Nazis which aren’t really in the same traditional line of vegetarians). Even if Newton, Darwin (Erasmus), Alfred Russell Wallace, Thoreau, Rousseau, and more, weren’t necessary strict vegetarians (some were) they all respected not only the vegetarian lifestyle but invited any discussions on the subject. That is in stark contrast to many intellectuals today (I am speaking specifically of many scientists) where even the conversation is looked down upon.

Another interesting illustration put forth by the book is the give and take between so-called western culture and India. Much of the evidence that it is possible to survive as a vegetarian (for the west) came from India, where examples were aplenty. Subsequently, Ghandi relied on the example set forth by the Vegetarian Society in England as an illustration of vegetarianism as a banner for rebellion instead of a sign of colonialism.

This book is overflowing with good scholarship and doesn’t feel preachy (until the last paragraph). It simply gives the facts, and they are very interesting. The discussion about Nazi Germany is particularly interesting. The influence of vegetarianism ranges from the French Revolution to India’s independence. I definitely recommend the book to anyone interested in the history vegetarianism and the history of many of the arguments put forth by anti and pro vegetarians.

Review: On the Road

On the Road by Jack Kerouac amazon

This is not so much a review of the book as much as a reflection on my re-reading of the book at this age and time, etc.

In mid-August the 50th anniversary of this influential book was released, complete with hardcover and the original review from the NYT. I am always intrigued, as many of my friends, in re-reading books we read in college or high school. This not only allows us to better remember these, usually, classic books, but also gives a completely new perspective given that we have some more life experience and are more able to get more out of the books.

So here was my opportunity to re-read and get a new appreciation for Kerouac. I remember liking Dharma Bums and more importantly there was also the release of the original scroll. The release of the original scroll (basically, first draft) is a great literary event where we get to see what Kerouac actually wrote, before editing.

At any rate, I had my opportunity and a nice evening so I got to reading.

Well, I must say, I wasn’t really that impressed. There is all the old beat language, the sexual promiscuity, and drug use and references, but it really, in my view, didn’t hold up very well to time.  For someone from my generation (I am 26), it is very hard to hold my interest when much of what makes the book interesting is its rebellion from the morays of the time in which the book was written.

I am not trying to be too harsh, just being honest. I had high hopes and just wasn’t that interested. If anyone reads this and disagrees, I suggest reflecting on your age (perhaps it is more relevant) and  reflecting on the last time you read it (sometimes fond memories of books have less to do with the book and more to do with the conditions under which we read them, not always, but sometimes).

For a more specific example (I won’t talk about the various “weed” references or other “beat” terms), many people seem to remember the book as expressing something about America (the land and people). I must say, I was very disappointed and the descriptions were not insightful.  The discussion of Chicago was much too short, in fact, the first long journey doesn’t invoke much description at all. More importantly, what descriptions of America are there, are not very inspired and I imagine a magazine would provide as much knowledge about the places as that found in On the Road.

I know this all sounds not very kind, but I must be honest, I expected to have a new found love and was let down.

Maybe another re-read many years from now will serve me better.