Daily Roundup

The internet today is practically seething with news of the rat-heart-jellyfish story, which is less absurd and far more interesting than this description makes it sound.

Researchers and bioengineers at Harvard have created what might be called a morphologically accurate jellyfish: a slip of a creature that pulses its way through liquid when an electric current is applied across it. We say “morphologically” because it’s nothing to actually do with a jellyfish; the creature is made from rat heart cells.

The news surrounding this, at first, seemed confused. The words “artificial jellyfish”, “rat heart” and “heart cells” have been bandied about without any real context to the issue. Take ABC’s reporting of the news, for instance. The meat of the matter makes its first appearance in the seventh paragraph (“Why do such an experiment?”). Build-up is all well and good, but establishing relevancy is a more important goal. The odd juxtaposition of jellyfish and rat hearts isn’t going to be really rewarding until you present the link — and soon.

Ed Yong, whose work I’ve been coming across more often recently, has a very nice piece in Nature which might as well be the polar opposite of ABC’s1. I very much appreciate the fact that both articles go beyond quoting the press release, but Yong’s is not only scientifically more informative, it’s also more… endearing, for lack of a better word.

A science writer’s comment thread I saw somewhere spoke about the importance of quotes from scientists, especially those who are apt to get excited about their work. I can’t think of a better representation of science than to quote these people, because science is so far from being a cold and mathematically driven discipline. It’s motivated by a need to improve lives, or to discover some even more fundamental truth about the universe, or to simply create something magnificent. Which is why these scientists are the best ones to get the story from. I liked the manifestation of this in the Ed Yong article:

In 2007, Parker was searching for new ways of studying muscular pumps when he visited the New England Aquarium in Boston, Massachusetts. “I saw the jellyfish display and it hit me like a thunderbolt,” he says… “I grabbed him and said, ‘John, I think I can build a jellyfish.’ He didn’t know who I was, but I was pretty excited and waving my arms, and I think he was afraid to say no.”

And soon enough, Yong gets to the point, in Parker’s own words:

“It’s exactly like what you see in the heart. My bet is that to get a muscular pump, the electrical activity has got to spread as a wavefront.”

Space, time and resources permitting, I’d love to be able to write an article like this. By the way, the extended version of the interview by Yong can be found here.

The other piece of news was something I should’ve written about over the weekend: researchers from Stanford U and J. Craig Venter Institute have simulated the entirety of an organism using a cluster of 128 computers.  The magnitude of this task needs to be emphasized: they simulated all known genetic processes of this humble bacterium that lives in human genitalia. Thus, they were able to track the entire life cycle of the organism — and, incidentally, open the way to creating better models for complicated processes like the genetic expression of human diseases.

“A lot of the public wonders, ‘Why haven’t we cured all these things?’ The answer, of course, is that cancer is not a one-gene problem; it’s a many-thousands-of-factors problem.”… For medical researchers and biochemists, simulation software will vastly speed the early stages of screening for new compounds.

Of course, this little guy has 525, while E. Coli has 4288 genes. It’s like a mathematical problem: if it takes 10 hours to simulate one division of an organism with 500-odd genes, how long will it take to simulate E. Coli? And how much extra hardware would that take?

What tickles me is this line:

In designing their model, the scientists chose an approach called object-oriented programming, which parallels the design of modern software systems.

I’m not sure what author John Markoff’s background is, but it certainly isn’t in programming (although I see he used to write for tech related things back in ’76. Punch cards, y’all). OOO is a very common concept that’s used in a variety of programming languages and isn’t nearly as exotic as this article makes it out to be. Every time you create a HelloWorld class in Java, you’re using object-oriented programming. The press release, however, has a better grasp of what constitutes cutting edge software technology. It’s quite fascinating, actually, and I need to ask my CS friends who have used CAD how exactly it might be adapted for more biological purposes.

1. I understand ABC isn’t a science magazine, but it’s still important to cover science news well and accurately. The New York Times covers science and politics as well as any other topic, for instance. Or maybe there are certain newspapers that specialize in science news? That would be an interesting thing to look up.

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