Blogs / The Loom

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.

I live near the Long Island Sound, in a landscape overrun with invaders from all over the world. My wife spends her free time ripping out Japanese knotweed from our garden. The Connecticut salt marshes are overrun with invasive Phragmites reeds.  Starlings descend on us like a hail storm. So I found it intriguing to discover some scientists who don’t consider invasive species to be all that big a deal compared to other effects we’re having on the environment, like habitat destruction and climate change. In today’s Science Times section of the New York Times, I have an article about some of their recent research, and their critics who think they’re missing the true dangers of invasives.

The article was not based merely on vented spleen. There have been a number of papers published on this issue in recent years. Here are a few…

Dov Sax and Steven Gaines, “Species Invasions and Extinctions: The Future of Native Biodiversity On Islands.” Proc Natl Acad Sci U S A. 2008 Aug 12;105 Suppl 1:11490-7. Epub 2008 Aug 11.

TJ Stohlgren et al, “The Myth of Plant Species Saturation.” Ecol Lett. 2008 Apr;11(4):313-22; discussion 322-6. Epub 2008 Jan 31.

Dov Sax et al, “Ecological and evolutionary insights from species invasions,” Trends Ecol Evol. 2007 Sep;22(9):465-71. Epub 2007 Jul 20.

Mark Vellend et al, “Effects of exotic species on evolutionary diversification.” Trends Ecol Evol. 2007 Sep;22(9):481-8. Epub 2007 Mar 7.

Anthony Ricciardi, “Are modern biological invasions an unprecedented form of global change?” Conserv Biol. 2007 Apr;21(2):329-36.

Behold Guilfordus horribilus, and shudder all thee ye who cross its path… (more…)

Recently I had the chance to talk to Richard Preston, author of The Hot Zone and other memorable books and articles. I was curious to learn how he reports his remarkable stories, getting inside the heads of scientists doing very bizarre work. Here’s our conversation, courtesy of Bloggingheads.tv.

Writing about the brain is one of the Black-Diamond challenges of science writing. We all think we know what’s going in our heads, and yet the cells and neurotransmitters and signal patterns don’t fit comfortably into our everyday metaphors. Linguist Mark Liberman at Language Log regularly writes devastating posts about how lousy a job journalists sometimes do writing about neuroscience news–especially when the research touches on our pat assumptions and stereotypes. (”See, women really do think differently…” etc.)

I’ve written a lot about the brain in the past (including a book about the dawn of neurology), but now I’m setting out to write a column every month for Discover about our gray matter. The first one is now online: it’s about how we perceive time. The first thing I had to do was throw out the metaphor of the clock, because it just doesn’t do a good job of capturing our brains’ beautiful strategies for gauging the flow of now into yesterday.

As I write these pieces, I hope that readers will leave comments–neuroscientists if you’re out there, and everyone else. I hope to get things right; I expect to get things wrong; and I’m prepared to learn along the way.

[Image: Fabiola Medeiros, reprinted under a Creative Commons licence]

The strange thing about E. coli, as I explain in my book Microcosm, is that it has played a central part not just in the modern science of life, but in the political conflicts over life. It may come as a surprise that a humble gut germ could get involved in culture wars. But you need only consider how much attention creationists have been lavishing on E. coli in recent years, hoping to use it as evidence that life did not evolve–that it was created or designed instead.

Originally, creationists claimed that structures in E. coli showed clear evidence of being created–they were complex, made up of lots of parts, and seemed to work like manmade machines. The flagellum–the tail E. coli spins hundreds of times a second–was one of their favorite examples. It reminded them of car engines, of outboard motors. This sort of thinking reached its climax a couple years back in the Dover Trial, in which parents claimed their school board was introducing religion into school in the guise of “intelligent design.” One lawyer joked that it should have been called the Flagellum Trial. In journalist Lauri Lebo’s excellent new account of the trial, The Devil in Dover, she recounts how one of the plaintiff parents came dressed as a flagellum, with a little tail poking out of her pants.

The school board lost, and in the scientific arena–where scientists publish their experiments in peer-reviewed journals–so have the advocates of a designed flagellum. The evolutionary history of the flagellum is becoming increasingly clear as scientists discover related copies of flagellar genes in other structures. But there are still people ready to sell you an intelligently designed flagellum throw pillow (or beer stein or apron).

Now E. coli poses a new quandary for creationists. As I wrote earlier this month, scientists at Michigan State University have been tracking the evolution of E. coli in their lab for 20 years. They’ve been experiencing natural selection as they’ve adapted to this environment, and in one of the twelve lines of these microbes, the bacteria evolved the ability to digest citrate. The lack of citrate metabolism has been, till now, a hallmark of E. coli as a species. The scientists don’t know precisely how the bacteria evolved this capacity, but it appears to have involved a series of mutations that happened over several thousand generations.

This new paper has apparently touched a creationist nerve. There have been two sorts of responses. One has been to downplay the finding. Unless E. coli actually evolves into a human being in front of someone’s eyes, then its evolution is insignificant. “It’s important for us all to remember that when we read science news that seems to ‘confirm’ evolution, it’s never a true threat to the biblical worldview and the creation account because God’s Word never changes but man’s fallible ideas do,” Answers in Genesis consoles us.

Some have responded by suggesting there must be some mistake in the experiment, perhaps even fraud. Perhaps there was some contaminating DNA that endowed the bacteria with the ability to feed on citrate, for example. Andrew Schlafly, who runs a site called Conservapedia that’s supposed to be a conservative alternative to Wikipedia, wrote a letter to the senior author on the E. coli, Richard Lenski. He demanded that Lenski “post the data supporting your remarkable claims so that we can review it.”

Lenski responded politely at first that as far as he could tell, the relevant data Schlafly wanted was in the paper, which Schlafly had not bothered to read closely. When Schlafly repeated his demands–and as the discussions on the Conservapedia site veered to accusations of Piltdown-Man-level fraud–Lenski wrote a barbed reply that’s definitely worth reading in full. You can see the whole correspondence at Panda’s Thumb or Bad Science.

It is surreal to watch people with Conservapedia claim to be champions of science. Conservapedia has a densely detailed entry for Young Earth creationism, and another for Flood Geology. But their entry for Big Bang Theory is tiny–and taken up in large part by the objections of creationists. The entry for parasites informs us of the young Earth view that parasites are the result of Adam’s sin. What’s not surreal is to see E. coli at the eye of the storm. It’s business as usual for the little bug.

My latest Dissection column for Wired.com takes on the old tug-of-war between Nature and Artifice. As I write in my new book Microcosm: E. coli and the New Science of Life, scientists began to manufacture strange versions of the microbe in the early 1970s. In 1974, for example, scientists engineered E. coli carrying DNA from a frog. The difference between such “unnatural” bacteria and “natural” ones may seem obvious, but today the dividing line is surprisingly tricky to draw, and will only get trickier. In my new column, I describe the first systematic attempt to do so. Check it out.

(Image from National Gallery of Art)

How old is the Grand Canyon? One answer is easy: a lot older than a few thousand years. A more precise answer is harder to get at, however. You have to climb into the caves of the Grand Canyon and read the geological clocks hidden there. For more, read my latest “Dissection” commentary at Wired.

Photo: Luca Galluzi at Galuzzi.it [via Wikipedia]

My latest story for the New York Times is up: it’s a sneak peek at the Encyclopedia of Life–a web site that will ultimately contain detailed pages about all 1.8 million known species. Right now it’s just a demo site, but on Thursday, there will be thousands of pages up, each with details on a different species. Will it reach its goal? As I point out in the article, previous attempts have failed. Their remnants are littered across the Web, such as the All-Species Foundation. But the scientists behind the Encyclopedia of Life have a lot of tools, like wikis and text-mining, that their predecessors lacked. Check it out on Thursday and come back here to tell me what you think.

Update, Tuesday 11 am: I just got an email newsletter from EOL saying the new version is now live. But at the moment, the site is down due to heavy traffic.

The history of science is rife with fateful meetings. The astronomer Tycho Brahe hires a young assistant named Johannes Kepler, who will go on to discover in Brahe’s observations the law of planetary motion. A bright but aimless British physicist named Francis Crick is introduced to a boisterous young American biologist named James Watson. The two soon discover they share a curiosity about a strange molecule called DNA. And on a warm afternoon in the early spring of 1838, the young Charles Darwin climbed into an orangutan’s cage.

That’s the start of my introduction to the recently published The Descent of Man: The Concise Edition. I’ve posted more of it at my web site. Check it out.

Why are modern families so small? Could it have something in common with peacock tails? A fascinating essay in the new issue of Science is the basis of my newest column for Wired. And man oh man, are the commenters freaking out. Judge for yourself.

The Natural History of the Only Child