Blogs / The Loom

Last night I strapped on a bow tie and shot out my tuxedo cuffs, got in the car, and headed to the upper West Side to celebrate a global cataclysm. Actually, I was helping to celebrate the geologist who discovered the cataclysm. Walter Alvarez was receiving the Vetlesen Prize, the highest honor in the earth sciences.

Under the magnificent rotunda at Columbia’s Low Library, we sat down to dinner. Michael Purdy, the director of Columbia’s Lamont-Doherty Geological Observatory, kicked off the event by explaining that Alvarez was winning the award because he had changed the way earth scientists view the history of the Earth. Later, Columbia president Lee Bollinger got up to present him with the award, declaring that Alvarez had shown how life was intimately connected to the cosmos. The real highlight of the evening, however, was listening to Alvarez himself.

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My experience with tuxedos has been limited to proms and weddings up until now, but today I’m renting a penguin suit for a most unexpected event: the geological equivalent of the Nobel Prize. Bet you didn’t know there was one! Actually, the Vetlesen Prize has been awarded every few years since 1959. This year’s winner is Walter Alvarez, who discovered the first clues that an asteroid plowed into the Earth 65 million years ago. The discovery was not just cool in and of itself, but changed the way scientists think about how surprising physical events can alter the course of evolution. I’ve spoken once to Alvarez on the phone, traded some email, and written the foreword to the new edition of his book, T. Rex and the Crater of Doom. So I’m excited to be suiting up today. I don’t think live-blogging is appropriate to the event, but I’ll report back once I’ve returned to civilian gear.

Image: The Vetlesen Prize site

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

Last month I wrote in the New York Times about Spore, a highly anticipated game that let you follow life from microbe to intergalactic civilization. I had a couple evolutionary biologists play around with it to get their reaction, and contact a couple others who had had a chance to play the game. They gave it positive–though decidely mixed–marks. In today’s issue of Science, John Bohanon describes the reactions of a number of other biologists, and they really don’t like it at all. Here’s what Ryan Gregory has to say:

“The problem is that the game features virtually none of the key ingredients of evolution as we understand it,” says Gregory. “There’s no shared common descent between species, since every single creature in Spore can trace its lineage back to a different single-celled organism that arrives from space.” Spore also lacks biological variation. “When you run into other members of your species, they are always identical clones of you.” Nor does it have natural selection. “There are no consequences for dying, since you just reappear at your nest.” Your organism does evolve, says Gregory, “in the sense that it changes over time, but it really has no bearing on how things evolve in the real world.”

I believe the article is behind a subscription wall, but you can check out a wiki Bohanan set up for an in-depth report card.

Evolution: Education and Outreach is a relatively new journal that helps teachers, students, and scientists teach evolutionary biology. I’ve just contributed a piece to a special issue on the evolution of the eye. I take a look at a couple examples of eyes evolving in weird ways. One example may be familiar to readers of this blog–the flatfish. The other example, illustrated here, is the stalk-eyed fly. The point I try to make in the piece is that these examples are not just a couple exhibits at a freak show. They tell us something important about the forces at work in evolution. Thankfully, the editors have made the journal open-access, so you can go read it for yourself.

One of Darwin’s lesser known obsessions was with faces–how we make different faces, and what they say about us. Today, psychologists and neuroscientists are discovering the hidden conversation between brain and face, with a lot of tools Darwin never had–MRI scanners, subcutaneous eletrodes, and Botox.

Botox?

Indeed. In fact, some recent studies with Botox raise the weird possibility that our national love affair with that face-freezing drug may be subtly altering the emotions of millions of people.

For more, check out my new column on the brain in the November issue of Discover.

[Illustration from Darwin’s The Expression of Emotions via Darwin Online]

Conservation Magazine is a snazzy publication from the Society of Conservation Biology that sports some great writers and great graphics. I was pleased to be asked to contribute a piece about some of my favorite living things–parasites. In particular, I look at new research that shows just how integral parasites are to the well-being of ecosystems. It’s just come out in the latest issue. Check it out.

I’ll be talking today on “Word of Mouth” on New Hampshire Public Radio at noon EST. The topic will be my new article on the biology of intelligence in Scientific American. Listen here.

Update: The segment is archived here.

In the latest issue of Scientific American, I have a feature on the biology of intelligence. (Read it online at sciam.com or carlzimmer.com) I’ve been fascinated by the subject for a long time, and I decided recently that the time was right to put together an article.

What’s the news? That there is no news.

Allow me to explain…

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The October issue of Discover is just out, and it has my second brain column (following up on my first, on the perception of time). This time around, I take a look at our unconscious, considering just how powerful it can be. But don’t get too disturbed by that inner zombie. Our conscious minds are not just helpless moviegoers in the theater of the brain. They have work to do as well. Check it out.