Tuesday, December 15, 2009

Google Celebrates 150th Birthday of Zamenhof

You may notice that today Google has a little Esperanto flag. This is in celebration of the 150th birthday of L. L. Zamenhof, the creator of the language. Esperanto is a fascinating little language, and works as diverse as The Lord of the Rings and The Origin of Species have been translated into it. It was the first foreign language that I managed to get a good reading knowledge of, and still the only one that I can read without a dictionary by my side. Many people give up learning languages because they don't see themselves getting to the stage of doing something interesting, like reading a novel in it. My success in reading Esperanto led me to develop my reading knowledge of French and German and my interest in more obscure languages such as Jersey and Sorbian. Not to mention Volapuk!

Monday, November 30, 2009

RIP Milorad Pavić (1929-2009)

Today Milorad Pavić died at the age of 80. He was the author of numerous novels, in particular the before-its-time hypertext Dictionary of the Khazars. The Dictionary of the Khazars was supposedly an encyclopedia about the Khazars, a medieval Eastern European tribe that accepted Judaism, but in fact it was a surreal work reminiscent of Borges in which the story was not told from front to back of the book but by following the references between articles. It would have been trivial to implement in HTML, but the book was written in 1984.

Tuesday, November 24, 2009

Happy Origin Day!

Today, 150 years ago, the first edition of Darwin's Origin of Species was published in London. I actually just learned that today -- while there was a lot of noise about the 200th anniversary of his birth last February, I didn't hear much about this ahead of time, so no, I didn't schedule a party like I did for Darwin's/Lincoln's birthday. Not that this seems to be the most opportune time for a party, given the oddly large number of people who attended the last one who now are otherwise occupied being new parents...

So I guess everyone's responsible for their own entertainment on this one.

But I'll leave you with some interesting links at least.
  1. Tired of the Origin's Victorian English? Read in in another language! Esperanto German French Spanish
  2. How about the Origin as a graphic novel?
  3. "Almost Like a Whale"/"Darwin's Ghost" This book, written by noted science popularizer Steve Jones, is an attempt to follow the structure of Darwin's Origin, but making adjustments to incorporate modern knowledge. While I'm a fan of the history of science and the value of primary sources, I understand that a lot of the difficulty in reading Darwin (besides his verbose Victorianisms) is that biology was a very different field in Darwin's day, both in terminology and outlook. Jones ably deals with this.

Monday, July 13, 2009

General Thoughts on the GRC, Part I

Well, since I guess I can't say anything specific about the talks due to the policy, I'll at least talk a bit about the topics that have been discussed so far in general terms.

1) Ken Nealson gave a nice keynote about the history of the study of metal reducing bacteria, being quite fair I thought towards the rival Lovley camp. He also ventured into what he himself called "crazy stuff" about electrobiology which I understand he might not want to be disseminated yet as he hasn't fully worked things through -- not for some secrecy reason. We also had a bit of a scare during the talk as a conference attendee suffered a seizure and paramedics had to be called. But fortunately it wasn't anything life threatening.

2) I was talking about my work on my phylogenetic pipeline APIS to a grad student of Brad Tebo's , and he mentioned "We had a woman from JCVI come up to discuss CMOP and she talked about that". Hmm. Could it be this talk?

3) On Monday morning, the main topics seemed to be Raman-Fish and Nano-SIMS. I hadn't heard of either technology before coming to the conference, but both are technologies used to track the metabolic activity of single cells. As my work in environmental microbiology is in large scale metagenomics, it is easy to forget that studies at the opposite end of the scale are also being revolutionized.

Sunday, July 12, 2009

GRC on Applied and Environmental Microbiology

So here I am at the campus of one of the Seven Sisters, Mt. Holyoke, for the Gordon Research Conference on Applied and Environmental Microbiology. I had intended on blogging this conference, as I do for most conferences I attend, but actually, I'm not sure of the legality in this case: The conference schedule says "All information provided at this GRC (formal talks, poster sessions, discussions) is considered private communication from the individual making the contribution and is presented with the restriction that such information is not for public use". This seems very strange to me. Why would anyone present *anything* at a conference if they want it private? Why have conferences at all? Maybe we can go back to the medieval alchemist model where we write our discoveries in code to prevent rivals from learning of them...

Tuesday, May 26, 2009

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).

Sunday, March 08, 2009

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!

Monday, February 16, 2009

"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.

Monday, January 19, 2009

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.