In the Land of Invented Languages

I promise that I'll return to science blogging soon, but I wanted to write something about a book I've just recently read -- Arika Okrent's "In The Land of Invented Languages". And after all, linguistics is a science, just not the one I generally write about.

Okrent is a trained linguist and it is interesting to see her take on constructed languages, which often get dismissive treatment in popular works on linguistics -- one senses than many linguists actually are proud to be ignorant of the subject, much as literary scholars often are about science fiction.

While Okrent gives an interesting historical overview of the subject, starting with such early works as Hildegard of Bingen's Lingua Ignota, her work really shines when she is describing the handful of modern constructed languages that have established user communities, albeit small ones: Esperanto, Lojban, Blissymbolics, and (yes) Klingon. Okrent not only has read up on these languages, but has learned their basics and attended conferences that these language communities held.

I realise that I'm somewhat of an ideal audience for such a book, as I am a guy who reads novels in Esperanto and who has tried (on and off again) to make headway into Lojban, but I think the book would also be of interest to those who have no contact with constructed languages. Okrent truly humanizes the people she meets -- even the much reviled Klingon speakers (whom, as Okrent notes, are stigmatized even among Trekkies).

Is the name "Sea Star" more accurate than "Starfish"?

It has become common in recent popularizations to suggest that echinoderms of the family Asteroidea should be given the common name "sea star" rather than the traditional "starfish". The complaint is understandable -- starfish aren't fish. In fact, humans are more closely related to fish, as they both are vertebrates while starfish are not. But is "sea star" actually a better supported name? A taxonomic analysis suggests not.

Let's consider stars, the sea, fish, and starfish.  How can we compare such diverse entities? Obviously not by molecular means. But we can return to the traditional means of cladistic characters. In this analysis I used:  1) Living 2) Primarily water 3) Non-trivial concentration of dissolved NaCl, and 4) presence of backbone.

These characters can be encoded in a PHYLIP matrix in the following manner.

    4    4
Star      0000
Fish      1111
Sea       0110
Starfish  1110

By standard parsimony this yields the following midpoint-rooted tree

So, while "starfish" is inaccurate, "sea star" is even worse!

"The Voyages of Charles Darwin" (1978)

Yesterday, I held a "Darwin/Lincoln" party for my co-worker friends at JCVI-West. To give a suitable background flavor, I played at a low volume episodes of the 1978 BBC TV series "The Voyages of Charles Darwin", in which the adventures of young Darwin are narrated (in "The Wonder Years" fashion) by old Darwin. 

This series hasn't been released on DVD yet (reasons found on the Internet vary from Creationist conspiracy to the more plausible explanation that the BBC doesn't actually own the rights to the incidental music, and re-scoring would cost too much.) At any rate, the series can still be found on the Internet in various forms -- even at the almost legitimate site Veoh.com. I think it is worth seeing, although the dated 1970s vibe does seep through -- one person coming to my party thought I was showing "Planet of the Apes" (to be fair, it was during a scene set in a rocky region of South America.)

Pictured, Charles Darwin (Malcolm Stoddard, right) reveals to his friend Joseph Hooker (Paul Chapman, left) his suspicions that species may not be immutable.

Happy Poe-day!

While the most anticipated 200th anniversary this year is the combined Darwin/Lincoln bicentennial on Feb 12th, they weren't the only famous people that were born in 1809. Today marks the 200th anniversary of Edgar Allan Poe's birth -- which occurred in Boston -- not a town that one usually associates with the man who became an editor of the Richmond, VA based Southern Literary Messenger and who died in 1849 in Baltimore.

I'm sure that other blogs and newspapers will bring up "The Raven", but Poe was more than a macabre poet and was more sane and rational than the narrators of his fiction and poetry, which many people confuse with Poe himself. So, I present you with other sides of the man that may be new to you.

1) Poe the book reviewer. Here Poe reviews Francis Glass' bizarre "WASHINGTONII VITA" -- a biography of George Washington written in pseudo-classical Latin!

2) Poe the literary theorist. In the "Philosophy of Composition" Poe describes how he wrote -- or at least how he *thought* he wrote -- which may not be the same thing at all -- shades of the debate over whether the cliched "scientific method" actually describes what scientists do in practice. 

3) Poe the biologist! Or at least Poe the biology textbook author --The Conchologist's First Book: or, A System of Testaceous Malacology, Arranged Expressly for the Use of Schools. There's actually a lot of questions about Poe's contributions to this -- apparently he based it on an existing text and was accused of plagiarism. 

The Bloody Olive

Not really typical material for my blog, but here's a thriller even more convoluted than "Nobel Son" -- and only ten minutes long! It's a Belgian-made short film from 1996, given new life thanks to Youtube. Excellent reproduction/parody of 1940s film-noir.

The science in "Nobel Son"

Last night I saw Nobel Son, the new Alan Rickman movie where he plays an arrogant chemist who wins the Nobel prize. I don't want to talk about the actual plot, which is one of those "wheels within wheels" over-complicated thrillers that everyone has seen before at least once.

Instead, I want to discuss the Rickman character -- Professor Eli Michaelson. Granted, the plot didn't really require him to be anything else than successful and arrogant -- he could have equally been a CEO or something without changing the movie much, but let's see how well the movie captured science and its culture.

1. Michaelson's  research. Apparently it has something to do with molecular fluorescence stimulated by lasers. Given that the 2008 Nobel Prize in Chemistry (which I'm sure was picked well after this movie was completed) , did deal with fluorescence, albeit created by Green Fluorescent Protein (GFP) rather than lasers, kudos to the scriptwriters.
2. Understanding of how grad school works. This the writers did not do so well. Early on in the movie Michaelson is established as unpleasant and unethical by showing him doing a quickie in his office with one of his grad students who is unhappy with her grade. I suspect the writers only have experience with undergraduate education. Grades just aren't a major issue in grad school. If the student were complaining about her project or authorship on a paper, this would have been more plausible.
3. Choice of reading material for a chemist. During the above mentioned quickie, an issue of Cell is clearly shown on Michaelson's desk. Yes, Cell is a major journal -- but for biologists and not chemists. An issue of Science or Nature (which publish across all branches of science) or indeed a chemistry journal, would have been more plausible.
4. Amount of Prize Money. The amount "$2 million" is a major plot factor in the movie. But would a Nobel Laureate actually get that much? The prize is currently $10 million SEK (US $1.2 million at present). Plus this amount is shared with the other winners in the category (The movie never says if Michaelson is sharing the award).

10th Anniversary of my Defense -- A Retrospective

On December 2, 1998 I defended my dissertation entitled "Exploration of microbial genomic sequences via comparative analysis", the somewhat vague title referring to a collection of projects that I worked on in Gary Olsen's (pictured) laboratory at the University of Illinois at Urbana-Champaign, most notably the CRITICA genefinder (which was, until a year or so ago, still in use at JGI), and one of the earliest genomic studies of thermostability.

My thesis committee consisted of Carl Woese, Tony Crofts, and Stan Maloy (now at SDSU; I run into him at seminars occasionally). 

I don't have any pictures of the defense or the lunch afterwords after owning to a sad accident -- my parents' camera had a broken lens, and in that pre-digital era, they didn't know anything was wrong until they tried to develop the film. Still, the day sticks with me in memory. I gave what was probably the best presentation of my career (probably because I had practiced ten times or so), and the questioning was very friendly (the serious questioning had been several years before at my prelim). 

I've worked a number of jobs moving to various cities in the name of science since those days -- a postdoc in Computer Science at the University of Waterloo,  a senior bioinformatics scientist at a now-defunct biotech firm in Montreal,  living in downtown DC while working in the microbial genomics departments of TIGR and its successor JCVI,  and now in San Diego, where I'm working at the west-coast campus of JCVI. Who knows where the next ten years will take me?