Monthly Archives: December 2010

Programmable Bacteria

A good bit of the news that I get is through Facebook, when geek friends post about something cool and techy. Like this article about programmable bacteria.

I want to figure out in what ways this science article succeeds and in what ways it doesn’t, and maybe — with my limited knowledge — talk about some of the nuances and the implications of it.

The CNN Article

The article begins with a short, snappy phrase — “bacteria that can be programmed like a computer” — and then goes on to describe how the logic gates are built from genes instead of wires and metal (I assume the quotation marks around “logic gates” isn’t to express skepticism but to illustrate that the genes were just acting like logic gates). Then the article talks about digital processing, and in just the third paragraph, leaps straight into the implications of such a programmable bacteria colony.

First of all, this is incredibly cool and more than a little exciting. If I’m understanding this correctly, the genetic code of simple organisms like bacteria can be programmed to act like the digital logic gates of an electronic circuit such as can be found in computers. So, say we want someone who’s diabetic (which usually means that you’re not producing nearly enough insulin, a hormone that controls the level of sugar in your body) to start producing more insulin — I suppose cells could now be “re-programmed” to respond to certain types of input (like too much sugar?) and that would artificially create insulin. Or perhaps they could just grow vats of pre-programmed bacteria which would produce natural chemical hormones.

The thing is, this sort of application is never explained in the article. They seem to simply go from “here’s a rough idea” to “here’s what we can do fifty years later”. “The findings hold promise for fields such as agriculture and the pharmaceutical industry,” says the CNN piece. But how promise? What promise?

Perhaps that might be easier to understand if we had been told what a logic gate actually is, how the genes could be rearranged to create such a logic gate, and what sorts of example inputs and outputs the bacteria colony would be producing. How is that colony linked up by the logic gates, anyway?

CNN, unfortunately, didn’t link to the academic paper in the article. Additional information on mathematical models, figures, etc can be found here. There are pros and cons to this: on the one hand, if you’re able to read the paper, you might realize that they were hyping it up a bit and we won’t be able to cure cancer by mere thought or something, decades into the future. On the other hand, a far more prosaic and realistic reason could be that most of these articles which are about to be published aren’t actually accessible without a (quite costly) subscription. Your average layperson certainly isn’t going to shell out thirty dollars for something that they — and this is the other crucial point — most likely won’t understand.

The Journal Abstract

But the journal abstract could tell us a few things, if we knew some basic knowledge. The journal article talks about how a NOR gate was constructed to drive promoters and repressors. This might sound like Greek, but honestly it’s not that bad. Logic gates just take in some inputs and spit out a function according to whatever they’re supposed to do. An AND gate only gives an output if both its inputs are happening at the same time. For instance, you’d go to bed only if you were sleepy AND you’d finished all your work. A NOR gate puts out some kind of positive output only if neither of the inputs is present. That sounds simple enough, but the important thing is that the NOR gate (and the NAND gate, which performs the exact reverse of the AND gate) is a “universal” gate: you can build any of the other gates, including the NAND, out of this one. That’s probably why the researchers chose to build that (again, the article doesn’t confirm that) and that’s why it’s a good thing that it appears to have worked.

And the repressors and promoters are, as far as I can tell, the means by which florescence was either turned off or turned on (respectively), which was the method the scientists were using to observe the success of their experiment.

The News Release

All that sort of information would’ve been really useful in an article of this kind, but CNN is not the only one to blame. The first source of information for science articles like this is usually the news release from the department or university itself, and it should list the purpose of the investigation, the people involved and their roles, the results and their implications. It’s basically like a science news article, except that the biases are clearly towards the scientists and the universities themselves; for instance, the press release for this included details about Voight’s previous awards or recognitions. It also included the crucial fact that Voight was not the lead author. It was, in fact, Alvin Tamsir, a fact that CNN left out entirely.

Now, looking at the news release, one thing jumps out at me: it’s not any more informative than the CNN piece itself. By this time, quite a few people know, even vaguely, that 1s and 0s form the basis of computation. The average reader is also aware that genes are what produce a lot of our individual characteristics, and that they can produce diseases which are sometimes impossible to cure (e.g. cancer). But the link between them is drawn imperfectly here. Yes, “any substrate can act like a computer”, but how is that substrate doing this?

So the press release takes on some blame as well for this sort of rather shoddy reporting. But that’s not quite fair, is it? Some CNN drone had to do their job and write this up by lunchtime and really they don’t have space or time.

If that’s your stance, go back to that article. Scroll down to the comments. If that’s representative of CNN’s readership, or representative of the average American, I’m seriously concerned for this nation.

And that’s why I think that the problem of mentioning examples, instead of vague declarations about revolutionizing pharmacy and agriculture, is something that needs to be fixed as soon as possible. Voight says, “It’s not that we’re trying to replace computers with living cells. But it means we could gain programmable control of everything biology can do. You’d like to be able to control all these programs.” To a rational, scientific-minded, reasonable skeptic, he sounds hopeful (and maybe a bit too optimistic). To those commentors, he sounds like Dr. Frankenstein. He should have either explained himself to his press team, or refrained from making hugely sweeping statements of the sort.

That, or the commentors could have been educated a little better, but that seems too much to hope for at this stage.

In the midst of this gloom and doom, however, I am able to offer some consolation: a better article! Here it is, at a site I’ve never heard of, called kqed.org.  Knowledge is power, folks. Enjoy! 🙂

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“Well, this is embarrassing.”

It’s practically a meme. Some of them are quite good. I’m talking about the 404 error page, of course.

If this doesn’t seem like “science writing”, let’s consider the general category they fall under: the “let’s make the Internet a friendlier place for dummies” type of wording on many pages.

For instance:

1. Google releases comics documenting its new technology. Incidentally, I just found this lovely little book on how the Internet works, courtesy of your favorite neighborhood search engine.

2. Facebook’s fairly detailed explanation of privacy settings, which have almost never been enough for those who’re bent on letting The Users know how they’re being subtly taken advantage of.

3. Grooveshark, like many other popular websites, keeps a nicely informal — but still pretty informative — blog.

4. Pandora, even with the annoyance of ads, strives to develop a certain pal-iness with the user: “Cool. We’re glad you like it. We’ll be sure to play more songs with similar musical qualities.”

I can actually remember my family’s first ever computer, a chunky Acer which I thought was the best thing in the world, so I think I can say this with some authority: the geeks are getting nicer. In a sense, that’s helping out the people who are still wary or unused to the Internet by providing something more than an impersonal facade to interact with. And, what with the explanations and transparency, I think this sort of friendlier content is really a niche arm of science writing, in a sense; it’s trying to make clear the gears and wheels of the process, or at least humanize some of them.

Which makes sense. The Web is becoming more of a community than a hierarchy, at least in that the content being developed gets extensively supported, vetted and vetoed by the users. That’s power right there, so it’s only fair and sensible that the most user-friendly sites reach out to their (overall younger) users in an attempt to get them involved in the process.

Integrity and Interest: Writing About Science for the Public

This semester, I did something I’ve been wanting to do for a year or so — I took a science writing course at my university. It seemed only natural, because it’s a mix of two of my favourite things to do. But the class was an eyeopener not just in the way that science could be written about for the public, but also the potential pitfalls that science writers and newspapers could fall into.

Those pitfalls can sometimes make scientists despair of the entire field of journalism. My cousin and I had a pretty strong argument about this at first, where he claimed that newspapers were a terrible way to be introduced to any new research and that a scientific paper was the only way to go. He also pointed out, quite rightly, that even papers as respectable as The New York Times are selective in their stories and in the presentation of the new research. It’s far more interesting to say that the latest in artificial intelligence has produced an android capable of conversation, but the reality might just be that a piece of software has been painstakingly coded with stock phrases that it is capable of sorting through and responding with.

One of my assignments for this course that I took was, in fact, to analyze a bunch of news articles published around the same time and based off the same news release, and the variety of reporting was astonishing. While the original article had stated that certain techniques of criminology were used to track sharks’ hunting patterns, many newspapers chose to publish that news as “Sharks Are Ocean’s Serial Killers.” The backlash from scientists, already quite tired of the Jaws prejudice, was immediate and sharp, and  I doubt that this is a unique situation.

But my cousin’s objections were, I thought, not quite fair to the journalists. So many of them really don’t have specialized degrees in some scientific field, yes. But if all scientists could effectively and engagingly communicate with the public, there would be no need for science journalism. The field is necessary simple because, caught up in their own work and enthusiasm, it’s been difficult for many experts in the field to spend the time crafting articles and essays that  draw the enthusiasm of the public.

So what’s the happy medium in this case? Is it really justifiable to spend four paragraphs explaining the standard model of subatomic particles before talking about how the Large Hadron Collider functions? Wouldn’t that discourage the average reader from continuing, when all they want to do is be told how this science will help them in the future?

But that’s another point that needs to be debated: what the average reader really is capable of. It’s tempting to think that we can respect the intelligence of the public (and, you know, be lazy at the same time) and not really spend time explaining the methodology and background of the experiment in question, but the truth of the matter is often that people — especially those in the United States — aren’t really comfortable with deep science. Health issues, for instance, and evolution, or even technology news are all things that the public has been exposed to over a long period of time. Much less so string theory. Newspapers, with their word limits and financial considerations, can’t honestly be blamed for prizing the understanding and continued support of the average reader over the completeness of the science.

Something my cousin mentioned is actually very valid in this situation. He said his main opposition to this kind of incomplete coverage of the science was that the taxpayer has a right to be completely informed about where their money is going. It’s their right to know that the government spending on, say, biofuel-producing algae was actually coming up with any discernible results that could help reduce their dependency on oil sometime in the future.

So here are the things that, both from experience and from this conversation, that I wish were better represented in science articles:

Explanations. If you’re going to talk about how there’s a new candidate  for gene therapy, then it only makes sense to talk about what gene therapy is in the first place — how “correct genes” can fundamentally change our DNA by entering our cells, piggybacked on a virus. That kind of explanation is even more crucial for more abstract physics ideas, but that’s where they’re also the toughest to execute.

Relevance. Gene therapy is directly relevant to us. But why the hell are we building a many-mile long particle accelerator that will use up a ridiculous amount of money, space and time? For instance, you could explain that the LHC’s purpose is to figure out if our current theory of the fundamental laws of physics holds — and if that theory could be further refined, perhaps we could manipulate them even more to our advantage.

Context. All right, so gene therapy sounds great  — but the greatest justice that can be done to something born in the scientific field is to rigorously contest it. What is its history? Does it have any past failures, and what can they teach us? What are, in comparison, its successes?

Caution. I sometimes think the nicest things about science articles is the sense of hope — not necessarily that everything will be cured or solved or rectified one day, but that everything will be understood. That nice thing is a double-edged sword, however. “Any minute now,” some articles seem to be saying, “we’ll be getting robot butlers. You just watch.” And that’s why qualifiers and uncertainty phrases are so very important — “scientists believe that this…”; “researchers are hopeful that in the future…”

One of the parting shots by my cousin was the fact that, since I am a  nominal member of the scientific community, it should be my responsibility to make sure that I served as an example by only referring people to respectable scientific publications. I dispute that, because I don’t think it’s doing anyone a huge favour by directing them to something totally incomprehensible, but I’d like to contribute to the general process of understanding.

This is why science writing is such a challenge and a burden at the same time. You’ve somehow got to inform, educate, caution and rejoice all in the same breath.

That challenge, really, is what attracts me to the field.

Why Hello There, World!

Isaac Newton supposedly named the colours of the rainbow by distinguishing between seven different wavelengths. But if you’ve ever seen a rainbow, you’ll know that though there are several particularly pretty colours, there aren’t necessarily seven. It has been said, in short, that Newton’s fascination with the number seven stemmed from his belief that seven was a Biblical, powerful number. Newton, in fact, was not a cold and logical calculating machine, but a man as deeply devoted to the mystical as to the material.

And science–or at least, the way we use it, discover it, and are continually befuddled by it–works in the same intersection between logic and society. We do try to generalize and quantify it, but at the same time, we impose upon it our personal views and interpretations of what science is or should be. And when we do have a hard and fast scientific rule, it’s not always clear that we’re applying it in the right–logically and morally speaking–way.

I’ve been interested in science ever since I won a bunch of science books in a storytelling competition. Paradoxical, but true. I love solving problems immensely and I love watching the way the world works. I also love explaining things, and I find it incomprehensible that not everyone is nerdy.

At the same time, I love writing. I like expressing my ideas clearly, concisely and convincingly, and on a large variety of subjects. But I’m particularly interested in the intersection between science and writing. A lot of people tend to regard science as boring, difficult, to grasp, abstract, or any combination of the above. I sincerely believe that this is not true, and I want to help destroy that preconception.

So the aim of this blog, in short, is:

a) To explain some of my favourite scientific concepts (and perhaps the readers’ as well, if I actually pick up any of those) in an interesting and comprehensible way

and

b) To sharpen my skills as a science writer, because it’s a field I want to enter some day.

I have some other writing that’s over in another, more personal blog that I’ll be porting over here, stuff that needs to be polished up but which I’d like to keep here as a record of my geekery. (To be honest I need to remind myself of some of the scientific concepts I come across every now and then, so I like looking back at these things.)

Now, think about this website. Think about bank upon bank of servers, all the information in the world coded into neat impersonal little 1’s and 0’s — from government secrets to sleepy chat conversations. Think about the millions of light signals, hurtling down miles of cables buried under a cold and wild ocean, connecting the world in a web of light and information called the Internet.

That’s science.