Two years ago, I wrote in the New York Times about scientists exploring evolution to discover the function of our genes. We share a 1.2 billion-year-old common ancestor with fungi, for example, and it turns out that fungi (yeast in particular) have networks of genes remarkably similar to our own.
Back in 2010, the scientists I interviewed told me they hoped to use this method to find new drugs. In today’s New York Times, I write about how they’ve delivered on that promise. It turns out that a drug that doctors have used for over 40 years to kill fungi can slow the growth of tumors. It’s a striking illustration of how evolution provides a map that allows medical research to find their way to promising new treatments. Check it out.
Like a number of other science writers, I’ve become increasingly interested (and concerned) about science’s ability to correct itself. (See my recent pieces about arsenic life, de-discovery, and dysfunctional science.) So I was intrigued by a new project launching today to encourage scientists to embrace the spirit of replication. I write about it at Slate. Check it out.
Last September, harbor seal pups in Massachusetts and New Hampshire started to die in droves. In today’s New York Times, I write about what killed them: a new influenza strain that evolved from shorebirds to seals, possibly as recently as last summer. While controversy swirls around scientists experimentally nudging flu viruses across the evolutionary between birds and mammals, Nature has been doing some experiments of its own. Check it out.
Here’s a video of a great talk about the evolution of whales that anatomist Joy Reidenberg gave at the recent PopTech conference. You may have seen her on the show Inside Nature’s Giants. Here’s my profile of Reidenberg this spring in the New York Times, in which I focused on what it’s like to take apart whales for a living.
I’m spending the weekend in Ottawa, where a couple thousand scientists have gathered for the Joint Congress of Evolutionary Biology. I’m drowning in a torrent of fascinating talks, on everything from sexually cannibalistic crickets to the future of the Amazon’s biodiversity. In the evenings, the meeting features high-profile talks–Friday night, the science writer David Quammen spoke about his career, on the occasion of winning the Stephen Jay Gould Prize. I have a particular interest in tonight’s talk, so much so that I’m going to live-blog it. The speaker is one Rosie Redfield, and she’ll be talking about the endlessly intriguing case of Arsenic Life.
Before Redfield takes to the stage at 7:30 pm ET, I want to write a short preface. In December 2010, rumors swirled for a few days that NASA had discovered alien life. When they finally held a press conference, the world discovered that a team of scientists had found a species of bacteria at Mono Lake in California that appeared to be able to build DNA out of arsenic. If true, it would be unlike any known life on Earth.
Rosie Redfield, a microbiologist at the University of British Columbia, read the paper after the embargo at Science was lifted, and didn’t like it. After she posted her complaints on her blog, I got in touch with her, along with a number of other scientists to see what they thought. Most of them didn’t like the paper either. I wrote about their collective reaction in an article on Slate, which was called “‘This Paper Should Not Have Been Published.'” (That was a quote from one of the scientists I spoke to.)
The authors of the paper, who were willing to hold a big press conference, give TED talks, and so on, refused to provide me any comments. They declared that all discussion must be restricted to peer-reviewed channels. Six months later, when Science finally published the arsenic life paper in a print edition, they also published a number of comments from Redfield and other critics.
Redfield and others argued that the arsenic life study had been poorly carried out. To put a scientific claim to the test, critics can try to replicate it. But, as I wrote in the New York Times, that’s a pain in the neck, and a lot of researchers would rather spend their precious time doing something interesting, rather than cleaning up other scientists’ messes. But Redfield decided to replicate the arsenic life study anyway. She had another motivation for doing so: she’s a big fan of open science, and so she used her blog to chronicle her experiences, from receiving the bacteria from the original authors to failing to replicate their results to posting her paper on Arxiv to getting her paper accepted to Science, where it’s now in press.
As Redfield notes on her blog, tonight’s talk presents a certain complication to the traditional way that high-profile journals publish papers. Journals like Science keep their papers under strict embargo, meaning that people are supposed to keep their mouth shut until an appointed time. Science provides pre-publication copies of the papers to journalists, usually a week in advance, so they can write up articles that can appear once the embargo lifts. So…if Redfield talks about her research, what does that mean for her paper? And does the fact that you can download it already from Arxiv make all of this moot?
7:36: Getting started. Redfield’s getting introduced.
7:38: “Rosie Redfield led the charge that NASA got it wrong.”
7:41 Redfield is starting: this is a story about the process of science, that starts with a press conference.
7:42 Redfield glosses over the utterly insane week of speculation that NASA had found aliens. Hey, she’s a microbiologist.
7:43 Why was this done? “The researchers were looking for exactly what they found.” (Not always a good thing in science.)
7:44: Looking for alien life is very expensive. So NASA is looking for terrestrial life that can help the search.
7:44: 2009 paper in Astrobiology: arsenci life team pointed out that arsenic is similar to phosphorus. So maybe early life could have used arsenic instead of phosphorus (in DNA for example). And maybe they’re still around.
7:45: Origin of life. You can start forward from early Earth, or go back from life today to figure out what first life must have had.
7:46: Early earth: simple chemicals created complex ones. Also, early Earth was “stinky.”
7:47 Comets delivered dirty water, loaded with polycyclic hydrocarbons.
7:48 All life today is all related. All life descended from a common ancestor.
7:50 Common ancestor of all life today: DNA genome, cellular, lipid bilayer, protein synthesis, many modern biochemical pathways.
7:51 There’s a gap scientists have yet to bridge from prebiotic Earth to last common universal ancestor.
7:52 What properties are essential in living things? Reproduction, heredity, and heritable variation that affects survival or reproduction. Redfield: “That spells natural selection.”
7:53 Natural selection probably kicked in long before our last universal common ancestor. First life could have much simpler metabolism. May not have been based on DNA. Life could have started as RNA. (Check out this story I wrote for Discover.)
7:55 Today, proteins do much of the work of metabolism.
7:57 Creationists seized on this open question. Evolutionary biologists claimed evolution doesn’t include origin of life. But RNA world gets closer to the origin, via evolution.
7:58 Back to arsenic: Poisonous because cells sometimes take up arsenic, which screws things up.
7:59 “Shadow biosphere”–a cool name, but almost certainly wrong.
8:00 Shadow biosphere hypothesis: weird life exists even today, hiding from scientists. Redfield: “This is extremely cool.”
8:01 Redfield recaps arsenic life experiment. Mono Lake bacteria kept growing as arsenic was swapped for phosphorus in medium.
8:02 Once Felisa Wolf-Simon could grow bacteria, brought in other scientists. Sophisticated tests such as NanoSIMS to show arsenic in (or near) arsenic.
8:05 Redfield was suspicious. NASA’s track record was not good, given Martian meteorite debacle.
8:06 Whenever Redfield wants to think something through, she blogs.
8:07 Press release has just gone out on arsenic life. There are TWO papers refuting it.
8:09 Redfield: Medium in arsenic life had some phosphate in it–same as ocean water.
8:11 Arsenic bacteria got fat. They couldn’t divide any more, so they swelled up.
8:13 Redfield argues that DNA of arsenic life bacteria that was already dirty with arsenic–arsenic not part of DNA.
8:15 Dan Vergano at USA Today is reporting on the new papers. Arsenic life paper lead author Felisa Wolf-Simon declares, “There is nothing in the data of these new papers that contradicts our published data.”
8:17 I forgot to link to my database of the responses from many critics. Here it is.
8:18 For some reason, some people made fun of Redfield for her dyed hair. It’s just gray at the moment.
8:19 Arsenic in DNA would fall apart very quickly. A big problem.
8:19 The bacterium in the arsenic life paper was not part of the shadow biosphere. It was just a member of a well-known genus called Halomonas.
8:21 The bacterium, called GFAJ-1 (Get Felisa Wolf-Simons A Job), is very, very, closely related to other Halomonas. Not much exotic evolution to become arsenic life.
8:22 No reason to think there would be natural selection for arsenic use, since Mono Lake has a fair amount of phosphorus (although a lot of arsenic too).
8:24 NASA suddenly switched from big press conference to shutting up. Felisa Wolf-Simon “had been been tweeting up a storm.”
8:25 Six months after the press conference, paper published, plus criticisms. Response of authors: “We think our research is fine.” –Redfield.
8:27 Redfield’s “selfish reason” for focusing on arsenic life: she blogs about her work, pursing open science. Important that the public see how science is done.
8:29 Redfield lacked all the expertise required for trying to replicate arsenic life. Blog post led to collaboration with experts who could do the job. (Actually, they volunteered their grad student!)
8:30 Redfield spent a month trying to get bacteria to grow, blogging all the way. Trouble with amino acids. Eventually, figured it out.
8:32 Redfield used better reagents with much less phosphate. Arsenic didn’t help growth. Arsenic life team was wrong.
8:33 Her DNA was stable for a couple months. Couldn’t have arsenic in it.
8:35 Redfield et al wrote up a paper, submitted to Science, and uploaded to Arxiv–because this is open science.
8:36 Science planned to publish on July 26.
8:36 Journals use embargoes to control how research is publicized. For more, read Embargo Watch.
8:38 Embargoes enforced by “vague threats.”
8:38 Weirdness of paper being on Arxiv for months and Science enforcing embargo. Redfield informed that embargo being lifted tonight.
8:39 I just told Redfield her paper has been up for half an hour. Applause breaks out.
8:40 Redfield: This is a story of serial failure. Lead author convinced of evidence without good research, senior authors didn’t provide supervision. Co-authors should have accepted responsibility. Reviewers failed, missed a lot of problems. Science failed in selecting reviewers.
8:42 “And finally, NASA failed big time.”
8:42 But the process of science did not fail.
8:45 Talk over. Question–will this episode change science? Redfield: If you blog about it, you mark that it’s your idea.
8:47 Peer review like democracy (as described by Churchill), is terrible, but the best we have.
8:48 Redfield: lots of “seriously flaky” stuff gets published, so we don’t have to worry about strangling science.
8:49 Idea of arsenic life “unlikely to be true,” but an “okay hypothesis.” You always fall in love with your own ideas. “It’s the ultimate high in science.” But you need self-discipline to test your hypothesis and see if it’s wrong.
8:52 That’s it, folks. Good night!
As I’ve mentioned a couple times, I’ve been working for a couple years with biologist Douglas Emlen on a new textbook about evolution, intended for biology majors. It’s scheduled to be published next month, and we’ve gathered some gratifying endorsements. Here are a selection:
“Exciting is a word not often used to describe a new textbook. But, by using powerful examples, beautiful images, and finely wrought prose Zimmer and Emlen have produced a text that not only conveys the explanatory power of evolution, but one permeated with the joy of doing science. Their text can only be described as an exciting moment for our field: it is an important accomplishment for our students and for evolutionary biology at large.” –Neil Shubin, University of Chicago, author of Your Inner Fish.
“A richly illustrated and very clearly written text, Evolution: Making Sense of Life brings forth the excitement, power, and importance of modern evolutionary biology in an accessible, yet sophisticated overview of the field.” –Sean B. Carroll, University of Wisconsin, Madison, author of Endless Forms Most Beautiful.
“If there was ever a book that makes it obvious why evolution is a fascinating topic—and a topic that goes to the core of understanding what biology is about—this is it. It truly makes you better understand and appreciate the biological world around us.” –Svante Paabo, Director, Max Planck Institute for Evolutionary Anthropology
“Two master craftsmen in the art of scientific communication have combined to produce an excellent basic text on evolution: it informs, explains, teaches and inspires. The illustrations are outstanding.” –Peter R. Grant, Princeton University
“Carl Zimmer and Douglas Emlen have captured in this stunning new book the excitement and richness of twenty-first century evolutionary biology. They describe clearly and elegantly not only what, but also how, we are learning about evolutionary processes and the patterns they produce. The writing is compelling, the illustrations beautiful and truly informative, and the balance between breadth and depth of discussion on each topic just right. This is a book that would make anyone think about becoming an evolutionary biologist today.” –John N. Thompson, University of California, Santa Cruz
“Beautifully written and lavishly illustrated, here’s a superb textbook that can do double duty gracing the coffee table. This book is bound to attract many more students into the field of evolutionary biology.” –Richard Lenski, Michigan State University
“This is not your grandmother’s evolution text. Breathtakingly illustrated, this book covers not only the usual topics in evolution – adaptation, drift, phylogenetic analysis – but also a host of new and exciting areas where groundbreaking research is occurring.” –Marlene Zuk, University of Minnesota
You can pre-order the book on Amazon here. And here is information at the web site at our publisher, Roberts & Company. Excitingly, they are also creating an iPad version of the book, with many interactive features. The app itself is free, and you can use it to download the first chapter (also free). The remaining chapters will be rolling out soon, with the price to be determined later. (No Android version, I’m afraid!)
1. Roadside evolution: Traveling to faraway lands to work on a story is one of the great privileges of this gig, but sometimes it’s nice just to head five minutes from your front door and go salamander hunting. That’s what I did for a story about evolution in our own time, which appears in the current issue of Environment Yale.
2. The Lehrer Affair. The best-selling science writer Jonah Lehrer made the sort of news a journalist wants to avoid: a number of passages in his magazine articles and books are closely to identical to stuff he’s written before. Journalist Seth Mnookin invited Jack Shafer (Reuters media critic), Deborah Blum (Pulitzer Prize-winning book author), David Quammen (prominent nature writer), and me to engage in a roundtable discussion of the controversy. Seth posted parts one and two last week, and part three goes up later today.
3. Do I look smart yet? For my latest Discover column, I explored the newest niche in neuro-marketing: brain drinks. You can now buy Gatorade-ish potions full of neurotransmitters, hormones, and other goodies, that are accompanied by vague promises of cognitive enhancement. I guzzled a sampling of smart drinks over a few days and wrote a column about it. Let’s just say, this was not a Hunter S. Thompson experience.
[Photo by me]
After half a year of stormy debate, we are finally getting to see all the gory details about how two teams of scientists produced some disturbing flu viruses. I’ve written about this unfolding story previously here, at Slate, here again, in the New York Times, and back here again.
In tomorrow’s New York Times, I step back and take a look at the two published studies, and talk to experts about what those studies do–and don’t–tell us about how likely we are to face a new flu pandemic in the years to come. There’s still a huge amount about the flu that we don’t know yet, sorry to say. Check it out. (I also spoke with Times editor Michael Mason on this week’s science podcast. Listen here.)
This month has seen a flood of new studies and reviews on the microbiome, the collection of creatures that call our bodies home. In tomorrow’s New York Times, I look at why scientists are going to so much effort to map out these 100 trillion microbes.
The microbiome is not just an opportunistic film of bugs: it’s an organ that play an important part in our well-being. It starts to form as we’re born, develops as we nurse, and comes to maturity like other parts of the body. It stabilizes our immune system, keeps our skin intact, synthesizes vitamins, and serves many other functions. Yet the microbiome is an organ made up of thousands of species–an ecosystem, really. And so a number of scientists are calling for a more ecological view of our health, rather than simply trying to wage warfare against infections.
A new book is out, called Zoobiquity: What Animals Can Teach Us About Health and the Science of Healing, coauthored by cardiologist Barbara Natterson-Horowitz and science writer Kathryn Bowers. They take a look at the surprising parallels between animal and human health. The Daily Beast asked me to review it, and you can read my piece here.
The facts that animals and humans share an evolutionary heritage, and that we can gain medical insights through a comparison between species, are not new. And Zoobiquity contains some misconceptions about how evolution works and how to analyze it. Nevertheless, I think the book well-worth reading. I learned a lot from it about things ranging from cancerous rhino horns to anorexic pigs.