May 9, 2008
Category: Microcosm: The Book
Just a quick note to say that, if all goes according to plan, I will be appearing on the Internets on bloggingheads tomorrow, and on the radio show Coast-to-Coast in the wee hours of Saturday night/Sunday morning. In both cases I'll be talking about--you guessed it--Microcosm. I'll be swilling coffee Saturday night because I'll be talking from 2 am to 5 am EST Sunday. If you're not quite such a night owl, I believe they'll archive it on their site.
A couple other Microcosm-related notes: Discover Magazine gives a nod: "With Microcosm, this award-winning science writer has turned out an illuminating biography of one of biology's most influential--and underappreciated--players."
Meanwhile, Larry Moran is going over the book with a fine-tooth comb and catching at least one mistake. Ouch. I knew I should have been more careful about how fast chromosomes replicate. Something to fix in the next printing...
Posted by Carl Zimmer at 2:44 PM • 0 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
At last we come to the fifth winning question about Microcosm, from Ceph. Once again, thanks to the ~240 people who entered the contest. I hope my answers to these five questions give you a sense of what my book's about and why I'm so excited by this little germ. If you want to learn more about it, and about life, pick up a copy.
Ceph asks,
What is your favorite thing that has been done to E. coli (making it glow, smell like bananas, etc)?
My answer below...
Read on »
Posted by Carl Zimmer at 1:00 PM • 1 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
Here's the fourth winning question about Microcosm, from Sigmund:
Creationists often point to the bacterial cell and say something to the effect of "the cell is so complicated it is highly improbable that it could have spontaneously formed - therefore God-did-it. Are there any particular features of E.coli that reveal simpler origins?
The answer below the fold...
Read on »
Posted by Carl Zimmer at 12:00 PM • 0 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
Now we come to the third winning question about Microcosm. Kenatiod writes,
Long ago, in bacteriology class, the teacher (an ex-nun at an ex-Catholic college) was telling us about the type "F" pili that are used to pass DNA so coli can have sex. One of the students asked "Why do they call them type F?" The teacher started to answer, but stopped, and then she turned bright red. The class start laughing, and then she did as well, and then someone asked, "What other kinds of pili are there?" She pulled herself together, said "Thank you" and class continued.
I would like to know both the answer to the original question, and also when in evolutionary history these tiny beings started having sex.
Read on for the erotic answer...
Read on »
Posted by Carl Zimmer at 11:00 AM • 0 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
Here's the second winning question about Microcosm, from Kevin:
E. coli is a bacteria commonly found in the intestines of some animals. What distinguishes the common and harmless strains from those that can cause illness and death?
A lot of people asked this question in the contest. But my sense is that most people think that E. coli is just a nasty germ. When I would tell people I was going to write about E. coli, they thought I was going to pen an expose of the food industry. It came as a surprise to them when I told them that they were carrying billions of E. coli inside them. [More below the fold...]
Read on »
Posted by Carl Zimmer at 10:00 AM • 0 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
If you're just tuning in, on Tuesday I offered five free signed copies of my new book Microcosm: E. coli and the New Science of Life to readers if they sent in a question. I was quite stoked to see the huge reaction. I can tell from the quality of the questions that the sheer volume was not just the result of the lust for a free book. While I can only answer five questions today, I think most people who asked one will find that parts of the book touch on it.
So--without further ado, let's dive in. (This is the first of five posts I'll deliver today.)
1. Frank asks:
Why E. coli? From a historical perspective, why do we study E. coli? There are countless easily culturable microbes out there, so how did the scientific community select this particular species as "the model" for microbiology?
This is one of the strangest parts of the story of E. coli. This microbe isn't just the model for microbiology. It's a model for a lot of the biology common to all living things, from the genetic code to the creation of new copies of DNA to the process by which food is turned into living matter. Scientists have identified the basic functions of most of E. coli's genes, which is a lot more than we can say even for human genes. If you type in "Escherichia coli" into PubMed, the search engine for the National Library of Medicine, you get 253,128 papers. Another favorite species, Drosophila melanogaster, sometimes (wrongly) called the fruit fly, brings up only 29,918.
So you might think there must have been some eminently rational plan to select E. coli to become the creature science knows best. But there wasn't. It was discovered by Theodor Escherich, a pediatrician. In 1885 he delivered a lecture announcing the discovery of a rod-shaped microbe in the diapers of healthy babies. He was struck by how fast it grew on all sorts of food--milk, potatoes, blood. Scientists in the early 1900s used it to study metabolism, but they also used a lot of other bacteria. It was one among many.
A few scientists in the late 1930s and early 1940s changed that. These were scientists who had especially deep questions about how life works. Max Delbruck wanted to know what genes are. George Beadle and Edward Tatum wanted to know how genes produced traits. They wound up with E. coli almost by accident. Tatum wanted to safe, fast-growing microbe that could build a lot of amino acids by itself. He and Beadle planned to blast such a microbe with X-rays to create mutations, and see whether the microbe lost the ability to make one of those amino acids. He chose a strain of E. coli called K-12 that had been isolated from a diptheria patient and had been used in microbiology classes at Stanford ever since.
Max Delbruck, down at Caltech, wanted to find something simpler than flies in which he could study genes. He discovered that another Caltech scientist, Emory Ellis, was infecting E. coli with viruses from sewer water. Ellis was really interested in viruses that might cause cancer in people, but figuring out how viruses infected E. coli seemed like a good place to start. So Delbruck and Ellis began to investigate how viruses could use E. coli to make new copies of themselves.
It certainly didn't hurt that E. coli was safe, grew fast, thrived in oxygen, and otherwise made life easy on scientists who studied it. But its success also came through a peculiar snowball effect. A young graduate student named Joshua Lederberg came to Tatum's lab to study his E. coli mutants, in the hopes of discovering that bacteria have sex. Tatum's bacteria just so happened to swap genes. Now scientists began to use their sex life to study genes, by pulling the microbes apart in the act and seeing which genes had made the jump. Scientists began to map E. coli's genes. They discovered in E. coli the switches that turn genes on and off. In other words, a new science called molecular biology was born. Soon scientists were choosing E. coli to study so they didn't have to reinvent the wheel. It helped that so much of biology is the same from species to species. As the French E. coli biologist Jacques Monod declared, what is true for E. coli is true for the elephant. But in an important sense, E. coli was the accidental victor.
Posted by Carl Zimmer at 7:00 AM • 1 Comments • 0 TrackBacks• View blog reactions
May 8, 2008
Category: Microcosm: The Book
Thanks to everyone who submitted the 240 or so questions about Microcosm, E. coli, and life in general. I'll pick five of them tonight and answer them tomorrow and start signing copies for the winners. And if you didn't enter, why not considering getting a copy anyway?
Posted by Carl Zimmer at 5:09 PM • 2 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
From the blog of Steven Johnson, author of The Ghost Map and Mind Wide Open
Go Buy Microcosm Right Now
Carl Zimmer may be my favorite science writer around today (others seem to agree), so I'm excited to report that his new book Microcosm: E. coli and the New Science of Life hit the shelves yesterday. I had the opportunity to read it in manuscript form, and it's really an exceptional book -- what Carl calls an "(un)natural history of E. coli" -- the world's most famous microbe. Having just published a book that partially starred a bacterium myself, I know how hard it is to make a book about microbial life engaging to human readers, but Carl pulls it off brilliantly here -- it's creepy, mind-twisting, and delightful all at the same time. It's the kind of book that literally expands your perspective on the world -- it helps you see how this alternative universe of tiny life forms is bound up crucially in our own day-to-day experience. So go check it out now....
Posted by Carl Zimmer at 3:01 PM • 1 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
Just a quick reminder--I'll be keeping the contest for a free autographed copy of Microcosm till 5 pm this afternoon. Think of a question about E. coli (and what it can say about life itself), and get in the running for a signed book. I'll post answers to the winning responses tomorrow by noon.
(Thanks to PZ Myers for a link from Pharyngula).
Posted by Carl Zimmer at 8:42 AM • 0 Comments • 0 TrackBacks• View blog reactions
Category: Evolution
In case you missed it, there's a great article in Smithsonian about hyena intelligence, focusing on the work of Kay Holekamp, the subject of my recent piece in the New York Times. The author, Steve Kemper, spent time with Holekamp in hyena country in Kenya, seeing just how brutal (and fascinating) life as a spotted hyena can be.
Smithsonian Magazine | Science & Nature | Who's Laughing Now?
update: link fixed.
Posted by Carl Zimmer at 8:25 AM • 2 Comments • 0 TrackBacks• View blog reactions
May 7, 2008
Category: Evolution
by the old man of the blogs, Andrew Sullivan, and even the editorial page of the New York Times. Who knew a few clever flies could win so many friends?
Posted by Carl Zimmer at 7:19 AM • 2 Comments • 0 TrackBacks• View blog reactions
May 6, 2008
Category: Microcosm: The Book
I'm in a celebratory mood. Microcosm is published today. In my mind, I can see the books moving out of warehouses onto trucks, off to book stores and front door steps. This morning I read a great review from Mykola Bilokonsky at Newsvine. ("What are you waiting for?" he asks.) And tonight I'll be having a little get-together, with the weather cooperating in splendid fashion. To spread the cheer, let me invite you to participate in a contest to win a copy of Microcosm that I will personally sign.
To enter, you just need to ask a Microcosm-related question in the comment thread. My book is specifically about E. coli, and generally about life. By illuminating how this microbe works, I end up exploring everything from synthetic biology to the possibility of extraterrestrial life to the evolutionary history recorded in E. coli's genome--a history that we share. For more information, you can check out the Newsvine review, or my previous Microcosm-related posts here, or my Microcosm page on my web site. Or you can just ask a question about E. coli that's been on your mind for years. I know you have at least one...
You can post a question between now and Thursday, 5 pm EST. I will then choose five questions to answer in a post on Friday, and I'll get in touch with the five winners for their addresses.
In the meantime, question away, and spread the word to anyone else who might be interesting in entering.
Update: Let's keep it to one question per entry, so that the question space isn't all gobbled up!
Update: The contest is closed. Come back Friday for winning questions and their answers.
Posted by Carl Zimmer at 9:50 AM • 243 Comments • 0 TrackBacks• View blog reactions
May 5, 2008
Category: Evolution
In tomorrow's New York Times, I take a look at the evolution of intelligence. Or rather, I look at its flip side. Scientists and the rest of us are obsessed with intelligence--not just the intelligence of our own species, but any glimmer of intelligence in other animals. I've written plenty of stories myself on this research, from the social brilliance of hyenas to the foresight of birds. But if these faculties are so great, then why aren't more animals smart? The answer, experiments suggest, is that learning and memory have nasty side-effects. They can even shorten your life (at least if you're a fly).
This story has an odd back-story of its own. If you report on scientific research on evolution, sooner or later you'll find yourself reading mind-blowing distortions of the science produced by creationists and people who make the same sorts of distortions and really really really don't want to be called creationists. Sometimes they happen to choose some interesting research to distort, which, for me, is the silver lining in gloomy creationist clouds.
A couple years ago I discovered to my surprise that Ann Coulter devoted several pages in one of her books to misreading an article of mine about the appendix. Coulter couldn't seem to understand that despite natural selection's ability to produce adaptations, nature is filled with flaws (like my own defective appendix). One source of nature's imperfection is the inescapable trade-off between the benefits some traits provide and the costs they incur. Coulter scoffed at experiments that suggested natural selection might not favor smart fruit flies. At about that point, I decided I had enough of Coulter and tracked down the original studies. I've been following this fascinating line of research ever since.
Posted by Carl Zimmer at 11:30 PM • 15 Comments • 0 TrackBacks• View blog reactions
Category: Microcosm: The Book
Tomorrow is the publication date of Microcosm: E. coli and the New Science of Life. I'll be celebrating by sending out some signed copies (details tomorrow), but in the meantime, here's an interview that just came out this morning about the book over at Newsvine, on the nature of life, how to navigate without a brain, and nature's indifference to the "natural."
Newsvine - Interview: Carl Zimmer, Author of Microcosm
Update 1 pm: This is cool. MSNBC (which owns Newsvine) put the interview on their science page.
Posted by Carl Zimmer at 10:46 AM • 3 Comments • 0 TrackBacks• View blog reactions
April 30, 2008
Category: Evolution
In my last post I wrote about how scientists are learning about the origin of animals by studying their genomes. One of the surprising findings of the latest research is that a group of animals called comb jellies (ctenophores) belong to the oldest lineage of living animals. Comb jellies look a bit like jellyfish--soft, tentacled creatures without brains or eyes but with a nervous system. As I wrote in the Boston Globe Monday, earlier studies had generally pointed to sponges as belonging to the oldest lineage. If comb jellies take their place, that may mean that the ancestors of sponges lost their nerve(s) and became anchored filter-feeders.
David Marjanovic then left this comment:
IMHO the tree is full of long-branch attraction. The position of the ctenophores is probably spurious.
So what's David talking about? Long-branch attraction refers to a pesky problem that evolutionary biologists face when trying to reconstruct ancient episodes in the history of life. In my article I only referred briefly to these sorts of challenges, but fortunately blogs give me a little room to stretch out.
Long-branch attraction is a new twist on a classic phenenomon in evolution called convergence. This happens when two lineages evolve into very similar forms. Legless lizards and snakes, for example, independently evolved a serpent body shape. The octopus eye forms images like a camera, just as ours do. Several strains of E. coli have evolved into disease-causing bacteria that invade intestinal cells. On the surface, two convergent species may look as if they share a close common ancestry. It can take some close scrutiny to discover that they are not.
A segment of DNA can also evolve convergenty in two lineages. Imagine that a particular segment of DNA in the ancestors of insects had a sequence, AAATAAA. Imagine that vertebrates had a sequence AATTGAA. It takes only one mutation in each lineage for them to both evolve into AAATGAA. Now they have an identical segment that they did not inherit through common ancestry.
This sort of convergence is unlikely to happen soon after two lineages split apart. But as more time passes--as branches get longer--it becomes more likely. Branches that are not in fact closely related get attracted to each other when scientists study their DNA. Hence, long-branch attraction. In the case of this new study, David is suggesting that sponges ended up looking more closely related to us than comb jellies because the DNA the scientists studied happened to evolve convergently.
I dropped a note to Casey Dunn, the lead author of the new study in Nature, and he fired back some enlightening comments...
Long branch attraction is one of the most common types of systematic error encountered in phylogenetic inference...It is the primary reason we say in the paper that the ctenophore result "should be viewed as provisional". Unfortunately, the Nature format is very restrictive in its length so we did not have room to explicitly discuss this issue, though we were very mindful of it and much of the experimental design was structured specifically to address it.
That design included finding lots of weird animals. Adding branches to an evolutionary tree essentially chops down long branches to shorter lengths, because the new species are more closely related to some of the animals than to others. That's why one of Dunn's colleagues fished up a second species of comb jelly when the startling results first emerged. The long branch of the original comb jelly now became split in two, reducing the amount of long-branch attraction.
Another possibility might be that the ancestors of comb jellies have evolved faster than other animals. Their rapid evolution would give rise to more differences between their DNA and the DNA of other animals. As a result, the more slowly-evolving animals, including sponges and us, would appear more similar. But when they measured the rate of change on each branch, the comb jellies didn't appear at all peculiar.
By taking these extra steps (and others), Dunn and his colleagues felt confident enough to go into print with their results. Fortunately, scientists can continue to test for the possibility of long-branch attraction by adding more species to the tree. Animals that belong to deep lineages are the best. The bizarre, balloon-bodied Trichoplax would be a good place to start, since its genome is already sequenced. Science, thankfully, marches on.
Comb jelly photo from bzibble
Posted by Carl Zimmer at 3:36 PM • 6 Comments • 0 TrackBacks• View blog reactions
April 28, 2008
Category: Evolution
Today in the Boston Globe, I write about how scientists are revising their understanding of the evolution of animals, thanks to more DNA and more weird animals. My favorite quote comes from biologist Mark Pallen, who says that the human genome would have been worthless without understanding how humans are related to other animals.
Unfortunately, this research has been subject to some poor reporting, and to some distortions from creationists. Ryan Gregory and Troy Britain set them straight, respectively.
Posted by Carl Zimmer at 11:56 AM • 5 Comments • 0 TrackBacks• View blog reactions
