Blogs / The Loom

As I wrote in my story in the New York Times today, much of your DNA is shut down by molecules collectively known as epigenetic marks. Roughly 100 sites are notable exceptions to this rule: your mother’s copy of these stretches of DNA are silenced, while your father’s are free to make proteins and RNA–or vice versa. This imbalance, known as imprinting, is utterly fascinating, and when the imprinting system goes awry–when dad’s genes start becoming active when they shouldn’t, or when mom’s genes go quiet when they should be active–the effects can be catastrophic. I first became familiar with gene imprinting while writing an article for the Times a couple years ago about a scientist at Harvard named David Haig, who has a theory for how it had evolved. He argues that gene imprinting is the result of an evolutionary tug of war between mothers and fathers, because mammalian parents have an evolutionary conflict of interest.

Now a couple scientists are extending this conflict theory to explain why so many imprinted genes are turning up in psychiatric disorders, ranging from autism to schizophrenia. They argue that the conflict between our parents plays out in our brains, too. This morning you can read about this provocative idea in my latest Discover column on the brain, or in this article by Benedict Carey in the Times.

These articles ought to come with a disclaimer: when we write about conflicts between parents, we are speaking metaphorically. We are actually referring to the rise and fall of different genes over millions of years, as natural selection acts on populations of thousands or millions of individuals. Just because you inherited imprinted genes from your mother or father doesn’t mean they sat down and drew up plans for using to maximize their own reproductive success (unless your father was Dr. Evil, I suppose…) Nevertheless, this new research does add an extra dimension to Philip Larkin’s ode to all miserable kids, which Larkin recites in this video (if you haven’t heard it before, just be warned that there’s some old-time Anglosaxon profanity along the way):

Things move fast these days for us science writers.

I’m writing this just after returning home from a radio studio in New Haven, where I was interviewed on NPR’s The Takeaway about my article in today’s New York Times on the gene’s identity crisis. (Speaking of fast, the segment is already archived for your listening pleasure here.)

And now I sit down to find that my next order of business is to respond to a pretty harsh judgment of the article that appeared overnight, from a scientist I respect.

Time for the fourth cup of coffee of the morning!

So: The scientist in question is Michael Eisen, a biologist at the Univiersity of California at Berkeley. Among the many interesting things Eisen studies are transcription factors, proteins that grab onto DNA to switch on and off the production of RNA and proteins. The sites where transcription factors bind to DNA lie outside the conventional boundaries of genes, realms that have sometimes been erroneously referred to with the blanket term of “junk DNA.”

A few weeks ago I took some journalists and press release writers to task about their description of a newly discovered site (known as an enhancer) that may have played a key role in the evolution of the distinctly human hand. They erroneously claimed that the enhancer had been previously considered useless junk DNA, and so the news was that it actually had a function. I pointed out that people have known about enhancers for about 30 years, and other important sites outside conventional genes for 50. I argued that the news about this hand enhancer was interesting enough without the messed-up history.

Eisen liked that post, but he thinks I’ve failed to follow my own advice in my new article, where I describe a lot of features of our DNA that don’t fit the classical concept of the gene, such as alternative splicing, noncoding RNA, and epigenetics:

Well, he needs to apply the same standard to himself. Alternative splicing was discovered in the late 1970’s. Non-coding RNAs in the 1980’s. And epigenetic effects were described over 50 years ago, with molecular mechanisms first worked out over 25 years ago…Science writers play a very important role as honest interpreters of science for the public. But if they don’t present science history accurately, they can’t be taken seriously as authorities on science present.

With all due respect, I would like to propose a hypothesis: Dr. Eisen blogged about my article without actually reading it all the way through.

I base this hypothesis on the fact that in my article I repeatedly pointed out that scientists knew of examples of alternative splicing and the rest long ago. So why write an article now? Because–as I said in the article–what were once considered exceptions to the rule have become the rule. What could be set aside when scientists reflected on the concept of the gene can no longer be ignored. This is a story not about one particular experiment that yielded one particular result, but the story of a large-scale change in the way scientists think. I like the way a scientist named Mark Gerstein put it during an interview:

 “The way biology works is different from mathematics,” said Mark Gerstein, a bioinformatician at Yale. “If you find one counterexample in mathematics, you go back and rethink the definitions. Biology is not like that. One or two counterexamples — people are willing to deal with that.”

I am not claiming that I’ve looked at the raw data from recent experiments and am telling scientists something they don’t already know. Just the reverse: I only wrote the story after talking to a number of scientists, some quoted in the article and some not, who all expressed a similar feeling that the weight of evidence today is leading to a remarkable change in how they think about genes. Nor did these scientists keep this feeling secret until I pried it from them–take a look, for example, at a new review in American Scientist co-authored by Gerstein that offers a new and improved definition of the gene, based on the research I describe in my article. I am also not claiming that all scientists feel the same way about the new results–for example, there’s a pretty spirited debate over how much of the noncoding RNA rolling off of our genomes does anything at all. And so I tried to squeeze a few quotes into the story to convey that disagreement.

Am I trying to have my cake and eat it too, as Eisen implies? I don’t think so, for the reasons I’ve laid out here. But maybe I’m wrong. I’m open to further criticism, but I still feel like these kinds of stories are worth writing. Some of the most interesting stories in science are move slowly on many fronts, rather than being one quick hit.

Over the past year or so I’ve been engaging in a bit of science-writing masochism. I’ve been asking a few short  questions and trying to get some answers from people who’ve spent years grappling with them. For example:

What is life? (in Seed)

What is a species? (in Scientific American)

What is intelligence? (also in Scientific American)

In tomorrow’s New York Times, I tackle my next question: What is a gene?

This article emerged out of a lot of conversations with my editor over the past few months. We marveled over the steady stream of intriguing studies on genetics that were being published–studies that were pushing us to expand our ideas about things we took for granted, like the very nature of genes. So I started talking to scientists who are looking closely at the human genome. Some are studying how the same stretch of DNA can spew out many different proteins. Some are looking at the previously underappreciated army of RNA molecules that create a shadow network in our cells. Some are studying heredity beyond DNA–the molecules that cling to DNA and control which parts get used to build proteins and RNA, and which are silenced (as wonderfully illustrated by the toadflax flowers shown here–identical genes, but different flowers). We talked about undead genes and carcasses of viruses that have been dead for millions of years. It’s a very long article for a newspaper, but trust me–I could have kept writing for a lot longer.

In fact, my piece is actually just the lead article to a package of stories exploring similar terrain, from Andrew Pollack on the search for RNA-based medicines to Natalie Angier on the philosophy of genes. Check them all out.

As I cryptically mentioned earlier, I’ll be talking about my article  tomorrow morning on the Takeaway, a morning news show on NPR. Check here for schedule information; you can also to the site for the podcast.

Image source: Nature Genetics

If all goes according to plan, at 6:50 am tomorrow morning I will not just be awake, but sitting in a studio in New Haven, talking on the Takeaway, a morning news show on NPR. Some stations will broadcast it live; others at later times. And it will also end up on their podcast.

I have to wait until later today to explain the topic; for now, let’s just say it’s a long view of cool biology.

[Note–that’s Eastern standard time]

On Thursday evening, I’ll be talking about Microcosm at the Guilford Free Library just down the road here in Guilford, Connecticut. It’s great to be talking in this lovely space on the Guilford Green, reopened at last after a year-long renovation. Here’s a flyer with more information. The event is free, but the library is taking reservations by phone at 203-453-8282.

Andrew, a marine biologist writes, “I call it ‘the balance of the deep.’ Two hydrothermal vent endemic gastropods to commemorate my first deep-sea cruise. The one on the top is Alviniconcha hessleri and the one on the bottom is Ifremeria nautilei.”

Carl: For more on these cool critters–which live at the bottom of the sea around vents that spew scalding water, getting their food from chemical-feeding bacteria that live inside special organs in their bodies–check out Deep Sea News.

Click here to go to the full Science Tattoo Emporium.

This morning as I was about to board a plane, my phone rang. A reporter with Scientific American wanted to ask me about my father’s campaign for the US Senate. She wanted to talk to me, a science writer, about my father’s experience with science as a Congressman from New Jersey and as a Senate candidate.

As a journalist, I’ve never written about my dad. For the most part, I think it’s a bad idea for science writers to dispense political opinions anywhere except over a beer. We’re entitled to our views like anyone else, but we should not blur the line between our views and the science we write about. If I am writing about DNA, I do not have to know the party of the geneticist I’m interviewing. Science is not Democratic or Republican. If science writers split their time between political commentary and straight science, readers may come to doubt their accuracy. That’s not to say that science writers shouldn’t demolish non-science disinformation when they see it, even if it comes from a politician. I don’t mind if people think I’m biased in favor of continental drift. But I do mind if they think I report things only because they fit my personal ideology.

I’ve tried to be particularly scrupulous when it comes to my father’s work as a politician. So when the reporter today asked to talk, I said I didn’t think it would be appropriate. Here’s what came of that exchange. It’s one of the stranger news hooks I’ve ever come across, but I was glad that the story revisits some of my father’s experiences with science. Yet I have to say that when I read my no-comment at the end, I seemed like a bit of a prude.

So, let me just note here that my father, the erstwhile chemistry student, helped me become fascinated by science. My father, the AP stringer, made me a better writer by showing me how any writing can always be made better. My father the candidate continues to show me how to conduct oneself with dignity and wit, to be fearless when there is reason to fear. That is my comment.

It’s already end-of-the-year-list time, and I’m delighted to see that Amazon has picked Microcosm for their top ten science books of 2008. I must confess I’ve been slow this year on reading science books. What little free time I’ve got I’ve signed over to trying to finish War and Peace before I die. I’m enjoying it greatly, but at the rate I’m going, it’s a toss-up whether I’ll hit my biological deadline. Of the books on Amazon’s list, I can certainly recommend Your Inner Fish, having reviewed it in Nature. But are there any 2008 science books missing from this list, in your opinion?

Julia writes, “6 years ago I decided to change my life and go back to uni to study medicine.  I decided that if I got through I was going to get a tattoo to celebrate – I wanted a tattoo that said something about me – about where I’d come from.  It took a long time to come up with the idea, but I came up with this – the neurone represents my medical degree, which synapses with my first academic passion - the biogeography of plants (so maybe I’m a bit of a freak).  To tie these together further, I chose plants that have medical (or at least pseudo-medical) uses – the dog violets can supposedly improve renal function (I want to be a nephrologist – many people think that makes me even more of a freak), and chamomile is known to have a calming effect (I thought it might help with all those stressful on-calls!).  Frankly, I chose the herb bennet because I thought it looked pretty!  I’d originally planned on having the neurone the other (right) way round, but my fantastic tattoo artist, Charlotte (she owns Venus Fly Trap in Edinburgh), thought it would look more root-like this way round, so I sacrificed some scientific accuracy for the sake of aesthetics.”

Click here to go to the full Science Tattoo Emporium.

Sweet review of Microcosm in the latest issue of the New England Journal of Medicine:

All in all, Microcosm is a phantasmagoric read that explains how our understanding of the nature of E. coli has helped to unravel the mysteries of our own nature and evolution. The book is impressive for the information it imparts and even more impressive for the ideas it provokes.

So there you go.

We humans spend a lot of time building tools out of pieces of the natural world. We started with sticks and stones, began to mine iron and other metals, and, just recently, learned how to manipulate the genes of living things. To make insulin, for example, biologists in the 1970s inserted human insulin genes into E. coli and turned the bacteria into living chemical factories. These days, scientists are trying to retool bacteria much more dramatically, treating them more like programmable computers than factories. It sounds simple enough, but it most definitely isn’t. All material pose challenges to tool-makers. Wood can rot, metal can buckle. And living things are maddeningly sloppy. That’s why it’s so impressive that scientists at the University of California at San Diego have just made the movie I’ve embedded below: glowing bacteria keep time with their blinks. Read the rest of this entry »

I’ve been quietly watching scientists flip out about Sarah Palin’s recent scoff about the US funding research on fruit flies in Paris–even Christopher Hitchens is now championing those fine insects today in Slate. But, thanks to a little grant-digging by PZ Myers, I discover that, in fact, all this brouhaha comes down to those dear friends of this blog, parasites. Frankly, if you wait long enough, everything comes down to parasites.

A lot of people thought at first that Palin was dismissing basic research on Drosophila melanogaster, which has yielded lots of profound insights about human biology. Palin herself hasn’t cleared up the issue, but on further reflection, the consensus is that she was complaining about research on the olive fruit fly. That insect is a nasty crop pest in the US. It’s also a pest in Europe, where people have been studying ways to control it–hence the need for funding research there.

So–how do they plan to control these pests? By unleashing a vicious, brutal death on their babies! (Apologies to any insect-rights people out there…)

Pests often become pests by getting shipped to new places where they can thrive without all the parasites and pathogens that kept them in check back home. So a promising way to rein them in is to go back to where they were evolved, and find some really nasty parasites that evolved with them. Happily, scientists have found a wasp in Africa, where the olive fruit flies came from, that appears to be specialized to lay their eggs only in the larvae of the flies. The wasps then drink up the larvae’s bodily fluids and crawl out, leaving behind the dried up corpse of their host. So the scientists have shipped the wasps to California and done a lot of testing on the them (you have to make sure they won’t go off and start killing harmless native insects). Their goal is to shower the wasps across the olive fields of America.

This may seem outlandish, but it’s actually a fairly well-developed technique for controlling pests. In my book Parasite Rex, I describe a devastating outbreak that threatened Africa’s cassava plant–a staple for millions of people across the continent. The cassava were being wiped out by mealybugs from South America. In the late 1980s, entomologist Hans Herren and his colleagues found a South American wasp and brought it to Nigeria. Then he had to figure out how to get the wasps to their hosts.

The wasps were put to sleep with carbon dioxide and then lodged in cylinders of foam rubber, 250 in each one, which were loaded into a magazine that had been custom-built for Herren at an Austrian camera factory. As the pilot passed over a field, Herren intended for him to be able to drop the wasps precisely. “It was like in fighter aircrafts. You know when to drop the bomb by looking at the crosshairs. We tried this over a swimming pool in Ibadan. We’d fly over and drop the wasps. At 180 miles per hour, we were able to get them in there.”

Once Herren figured out how to drop his parasitic payload precisely, he started showing millions of wasps on African farms. After a few years, Herren had driven down the mealybugs to tiny numbers.

So please, my fellow Americans, think kindly on parasites this election year. If handled right, they can save your dinner.

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