"Bubbly" Pauline & the $1000 genome

I'm currently reading Kevin Davies' new book, "The $1000 Genome", which is an account of the various players trying to bring down the cost of human genome sequencing to commodity levels that would make having your own genome sequenced a practical reality. Although I know some of the technologies described in the book from my work, Davies' book focuses not only on the technical side but on the business/economic side as well and is written for the general reader. It's quite well written and interesting, and I recommend it. But what made me burst out laughing was encountering the following line:

"An important next step was to compare the data from Venter and Watson, which was first done by Pauline Ng, a bubbly Venter Institute researcher."

Pauline is a colleague and friend of mine who now leads a group at the Genome Institute of Singapore. We wrote a review chapter together on the human microbiome in a book that should be coming out soon. I suppose if you had to sum her up in a single adjective, "bubbly" works. But I guess I find the idea of someone I know being reduced to a journalistic cliché kind of amusing.

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).

A Life Decoded: My Genome: My Life

First of all, I'll get the required whining over the title done with -- yes, RPM, myself, and TR Gregory all have written about our annoyance with the terms "decoded/deciphered/cracked" in relationship to genomes, but there's a good chance that the title was thought up by the publisher. I would have called it "A Life in Sequence", but oddly enough, nobody asked me.

Now that that's done, how was the book? Pretty good (and I'm not just saying that because Craig's my ultimate boss and could fire me, honest -- he'd have to know who I was, for starters). It's a bit snarky in places, and some of his opponents come off as caricatures, but it's entertaining in much the same way as The Double Helix was.

The book is written as an autobiography, with bits of relevant genome information inserted in -- the gimmick is that this is the first of many "molecular (auto)biographies" that will interpret lives in the context of genomic sequences and the alleles the subject carries. Right now, it is a gimmick (although an amusing one), but I can see how in the future it might really be informative.

Much of Craig's working class youth and experience in the Vietnam War have been covered by various media stories before, but it is nice to hear it straight from Craig -- for one thing, it clears up the confusion between the shark and sea snake stories -- often these anecdotes are wrongly merged into one story.

What was new to me was learning about his pre-genomics scientific career. I had no idea that Craig's background was in biochemistry, for example. He credits that with helping him getting the early (notoriously temperamental and unreliable) automated sequencing machines to work when others, mostly from genetics and molecular biology backgrounds, couldn't.

The book is also interesting for some rather open and telling quotes -- probably my favorite is

One of my critics, John Sulston, objected that I wanted to have it both ways: "to achieve recognition and acclaim from his peers for his scientific work, but also to accommodate the needs of his business partners for secrecy and enjoy the resulting profits". I plead guilty, along with the rest of humanity, to committing the most heinous crime of both wanting my cake and eating it.

The rest of humanity indeed. Later Craig shows that many in the "holier-than-thou" public genome project also had links to the biotech industry; their primary difference from Craig seems to be that they tended to hide their conflicts of interest rather than openly declaring them.

Some of Craig's interpretations may be a little off base -- at one point Craig prides himself for not having the tenure system at his institutes on the basis that "the second rate people who thrive in a tenured environment like nothing more than to surround themselves with more mediocrity and drive out those who might excel and reveal the shortcomings of the entrenched". Well, perhaps. But the simpler explanation might be that tenure is rather hard to give when everyone is working off soft money which could disappear in the next funding cycle. And there has to be more to the story that Claire was the one who suggested merging JCVI and TIGR. In what context?

But in general, Craig's observations are dead on. Venter's opponents have tried to spread the myth that he's out to be "the Bill Gates of Biology", and whatever faults the guy has, his motivations are a lot more complicated than just the pursuit of money. Shreeve's "The Genome War" covered some of this, but it is nice to finally hear Craig's story from himself.

The Third Domain

Tim Friend's recent book The Third Domain is an odd book on two levels -- first of all, the story that one would think it tells, that of Carl Woese's discovery of the Archaea, the initial hostile reaction that the discovery met with at the hands of the scientific establishment, and its eventual acceptance by the majority -- makes up only one chapter (chapter 3) of the book. The rest of the book mostly follows field microbiologists like Karl Stetter and Eric Mathur as they collect samples (often, but not always, of archaea) from hot springs and thermal vents. Secondly, rather than being one unified whole, each chapter reads as its own story (which it may well have been; Friend is a former USA Today science writer and may be simply fleshing out articles he's already written). I'm of two minds about this book; as a evolutionary microbial genomicist (and one who has had the honor of working with Woese), I'm glad that there's a new book for the general public that acknowledges that microbes are worth studying for things other than their effect on human health; but on the other hand, I can't help but wonder if the story of the Archaea couldn't have been told in a more engaging manner. Bill Bryson, in his A Short History of Nearly Everything managed to tell Woese's story (if a bit too simplified) in an exciting chapter there. In conclusion, The Third Domain is worth a read (especially if you are interested in the subject), but the definitive book on Woese and the archaea has yet to be written.

The Difference Engine

I've just finished reading Doron Swade's "The Difference Engine: Charles Babbage and the Quest to Build the First Computer". In it, Swade (a curator at London's Science Museum) tells two stories: the first is a biography of Charles Babbage, the 19th century polymath who designed a series of mechanical computing devices that were never built, and the other is Swade's own story of building a working version of Babbage's Difference Engine No. 2 for the Science Museum.


I've long been fascinated by the idea of clockwork computers, and had a general idea of Babbage's story, but Swade dispels some common myths that have surrounded him. For example, one often reads that 19th century manufacturing techniques were too crude to create parts with the required tolerances, but Swade's studies on the surviving parts of Babbage's unfinished engines shows that they were sufficient. Rather, the issue was political and personal. Babbage's constant redesigning of his engines rather than creating a working version of any of them, combined with his skill at making enemies in influential places, meant that the British government finally lost patience and discontinued funding. Swade also deflates the romantic idea of Lord Byron's daughter Ada Lovelace being the "first programmer"; While Ada did provide examples of engine programs (really just algorithms) in a series of notes to her translation of a French article about the Analytical Engine, they unfortunately seem to be paraphrases of Babbage's own work.

Oh -- one last note -- the title may lead to confusion with William Gibson & Bruce Sterling's alternative history novel also entitled "The Difference Engine" in which Babbage Engines were built and started the Information Age a century early. That's a different book!