Blogs / The Loom

Not too long ago I was interviewed for episode of the radio show Radiolab. Jad Abumrad and Robert Krulwich led me to a windowless cubicle where they then grilled me for a long, long time. From that interrogation, they produce a medley in which I say:

“Sloppy, sloppy, noisy, chaos, jumble, chance, sloppy, sloppy…”

Fortunately, they also saved a little more of our conversation, which was on a topic near and dear to my heart: the noisiness of life. It’s a subject I discuss at some length in my book Microcosm (ahem–paperback coming out on July 14–ahem). To wit: if you think that down at the level of molecules and atoms our bodies are just regular clock-like devices that go tick-tock-tick-tock, you’d be wrong. It’s a sloppy, noisy process, out of which it’s amazing that the regularities and predictabilities of our lives emerge.

The episode that Jad and Robert produced, called “Stochasticity,” (listen here) looks at the many roles chance plays in our life–from the level of cells, where I tend to lurk, to the myth of the hot hand in basketball.

Of course, like any self-absorbed starlet, I must say now that some of my best work was left behind on the cutting-room floor, or at least inside somebody’s hard drive. It was inevitable, given how cool and multi-faceted the mystery of biological noise can be. For example, I talk about noise filters on Radiolab, but I didn’t talk about one of the most important ones, which keeps signals clear in in our brains. If you want to read more, check out this piece I wrote last year for Wired. And I also didn’t get to explain that noise isn’t just something to get rid of, just an unalloyed bad thing. In fact, life has evolved to use noise to its advantage. Even E. coli knows how to play the odds like a skilled gambler, as I explained last year in the New York Times.

And if you want to head straight for the scientific literature behind this story, a great place to start is with the wonderfully-named 2008 review, “Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences” (pdf at author’s site)

[Image: jaxpix on Flickr, via Creative Commons Licence]

Okay–for real, this is the last post before the weekend. The Royal Society has posted its longlist for their science book prize, and Microcosm is on it. Here’s the full line-up, with comments from the judges. Excellent company to be in.

What the nose knows: The science of scent in everyday life by Avery Gilbert (Crown Publishers)
“It’s a really original subject matter – how many smells can you actually distinguish and how smells evoke emotions. What’s so good about it is that the book’s not just about science – it’s about the science of everyday life.” (Deborah Cohen)

Bad science by Ben Goldacre (Harper Perennial)
“It proves the theory that science can be funny.” (Danny Wallace)

The Age of Wonder: How the Romantic generation discovered the beauty and terror of science by Richard Holmes (HarperPress)
“To my mind this is the most original book on our long-list. Holmes has thought about the subject in a way that other people haven’t done, and it’s beautifully put together.” (Philip Ball)

Living with Enza: The forgotten story of Britain and the great flu pandemic of 1918 by Mark Honigsbaum (Palgrave Macmillan)
“More people died due to the1918 flu pandemic than died in the First World War, so it’s amazing that we haven’t heard more about it. The book is also really relevant for the times in which we live.” (Maggie Aderin-Pocock)

Quantum: Einstein, Bohr and the great debate about the nature of reality by Manjit Kumar (Icon Books)
“This is the history of quantum mechanics, which I think is one of the most romantic stories in the history of science. It’s a story that’s tough to grasp and this is a pretty good shot at it.” (Tim Hunt)

Strange fruit: Why both sides are wrong in the race debate by Kenan Malik (Oneworld Publications)
“Probably one of the most controversial books on the long list. It’s a debate people tend to steer clear of so it’s interesting to see it addressed in a scientific way.  A book that challenges and provokes.” (Deborah Cohen)

Decoding the heavens: Solving the mystery of the world’s first computer by Jo Marchant (William Heinemann)
“This is the extraordinary story behind the world’s first computer: this thing called the Antikythera Mechanism which is from ancient Greece, and was found under the sea on a shipwreck. This is a great detective story, unravelling the mystery behind this strange contraption which appears to be so far ahead if its time” (Deborah Cohen)

The drunkard’s walk: How randomness rules our lives by Leonard Mlodinow (Allen Lane, Penguin Press)
“We all find this book intriguing. It’s a fascinating look at what happens in our lives and whether our efforts and hard work actually mean anything, or whether it’s down to whim and blind chance. It’s an immediately interesting concept well written, meaningful and fun.” (Danny Wallace)

Physics for future presidents: The science behind the headlines by Richard A Muller (WW Norton)
“Is it really possible to put a hydrogen bomb in a suitcase? What do you do if a nasty white powder slips out of an envelope? This book tackles questions about real terrorist threats using quantitative information.  One could easily imagine it on Obama’s table.” (Tim Hunt)

Your inner fish: The amazing discovery of our 375-million-year-old ancestor by Neil Shubin (Allen Lane, Penguin Press)
“If you came round to my house and described this book to me I’d ask you to leave. But in print, it really works.” (Danny Wallace)

Ice, mud and blood: Lessons from climates past by Chris Turney (Palgrave Macmillan)
“Climate change has always happened, so by looking at the climates of the past we can perhaps understand where we might be going wrong. Just taking a snapshot in time is too localised, which is why this book is so important.” (Maggie Aderin-Pocock)

Microcosm: E. coli and the new science of life by Carl Zimmer (William Heinemann)
“The bacteria in your gut is a pretty unlikely topic. But Carl Zimmer turns it into an exploration of what a living organism is, and opens up the mechanisms of life.” (Philip Ball)

The universe in a mirror: The saga of the Hubble Space Telescope and the visionaries who built it by Robert Zimmerman (Princeton University Press)
“Hubble is approaching the end of its life, which really has been an exciting saga. So reviewing that life story is a wonderful thing to do. We see the time, the energy and the passion it takes to build something that amazing and also the understanding that it gave us of our universe.” (Maggie Aderin-Pocock)

To explain the origin of life, scientists seek to explain the origin of its components. The three most important of these are RNA, DNA, and proteins.

Just about all life today uses DNA to encode its genetic information. The only exception are viruses that use a single-stranded version of DNA, known as RNA. The rest of us have RNA in our cells as well, but it carries out other functions. Some RNA molecules are copies of genes that our cells use as templates to build proteins; others can silence genes or act as sensors or help to build proteins. As I wrote in an essay published in Science in January, this sort of evidence has led a number of researchers to argue that life as we know it, with DNA, RNA, and proteins, started out with just RNA. In the so-called RNA world, this versatile molecule acted both like DNA (storing genetic information) and proteins (carrying out chemical reactions, such as building new RNA molecules). It’s a big hypothesis, and certainly not simple to test. No one has discovered any truly free-living RNA-based organisms, and so if the RNA World did exist once, its inhabitants may have been driven extinct when some of them gave rise to DNA-based life. And there’s another big question: if there was RNA-based life, where did the RNA come from?

One possibility is that the raw ingredients on the early, lifeless Earth reacted with each other and produced RNA. For 40 years, scientists have been investigating the chemistry of those ingredients–stuff like formaldehyde and cyanide–to see if they could indeed combine into the first biological molecules. It’s been quite a struggle–but it turns out that it was a struggle the scientists brought upon themselves. They tried to make RNA the obvious way, but nature doesn’t care what we consider obvious.

RNA is a word-like molecule, with four different letters that can be combined into a vast variety of strings. Each letter is called a ribonucleotide. It has two parts. One part lets the ribonucleotide bind to the ribonucleotides on either side, to form a backbone. It’s made of phosphate and a sugar called ribose. The other part is the nucleobase, which comes in four different forms and encodes genetic information.

So it seemed obvious that if indeed RNA emerged on the early Earth, its two parts must have emerged first. Scientists discovered reactions that suggested that nucleobases can indeed form from prebiotic molecules, as can the riboose-phosphate backbone. But when it came time to join together the two parts, the scientists hit a wall. The two molecules just don’t like each other much. Their dislike of each other led some scientists to look into the possibility that life did not start out with RNA, but with another molecule that doesn’t exist anywhere on Earth today. Later, RNA replaced that mystery molecule, and then later still DNA and protein evolved.

But as I explained in my Science essay, University of Manchester John Sutherland thought it was too soon to rule out the possibility that life had started out with RNA. He began to look for other routes from prebiotic chemistry to RNA besides the obvious one. Today, in Nature, he and his colleagues report that they found it.

In their paper, they published a kind of chemical road map that sums up what they did. Don’t be put off–I’ll explain the lay of the land below.

The blue arrows represent the obvious route to RNA, going from prebiotic compounds (marked here by 7,8, and 10) to nucleobases (3) and ribose (4). And the big red X shows the point at which this route fails.

Sutherland and his colleagues started with the same ingredients, but cooked them in a different recipe, marked in green. Instead of trying to build the two parts independently, the scientists instead built a single molecule that had more and more components of the two parts already in place. They used just four reactions, all of which worked efficiently, to get one of the four ribonucleotides, known as cytidine. At the end of the process, the scientists zapped the mix with ultraviolet light (something that would be easy to come by on the early Earth, unprotected by an ozone layer). They eliminated some of the unwanted side products and turned some of the cytidine into another unit of RNA, known as uracil.

In an accompany commentary, Jack Szostak of Harvard calls this experiment a “tour de fource.” Of course, it doesn’t answer all the questions about the RNA World–for starters, scientists still have to synthesize the other two letters in RNA’s alphabet. But it does show how careful scientists must be not to declare things impossible. Sometimes they just need to redraw the map.

Sources:

Powner et al, “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions,” Nature 2009, 459:239  doi:10.1038/nature08013

Jack Szostak, “Systems chemistry on early Earth,” Nature 2009, 459:171 

[Image: MuppetWiki]

There’s a piece in the Wall Street Journal today about biohacking: people experimenting with genetically engineered microbes and viruses at home. It tries to inject anxiety into your brain right from the start, with a headline,  “In Attics and Closets, ‘Biohackers’ Discover Their Inner Frankenstein–Using Mail-Order DNA and Iguana Heaters, Hobbyists Brew New Life Forms; Is It Risky?”

I was surprised, however, to discover that the reporter does not mention the one time that somebody actually got arrested and charged with biohacking. At last year’s World Science Festival, I moderated a panel with the artist Steven Kurtz, who had just finished navigating a Kafkaesque experience with the FBI for having a PCR machine and some harmless soil bacteria in his house. While we certainly need protection against bioterrorism and risky experiments, we definitely do not need the sort of ignorance of basic biology that was on display in the Kurtz affair.

Eyebeam, the New York gallery that hosted the panel, later posted the talk in several parts on YouTube. I’ve embedded them below. Kurtz has a sad and surreal story to tell.

I went to the Los Angeles Book Festival this weekend and was very impressed. Bibliophiles swarmed over the UCLA campus like literary army ants, and it seemed like every event of the day was packed. That included the panel discussion I was in, about science. My co-panelists were Avery Gilbert, a fellow finalist for the LA Times Science Book Prize, and Leonard Susskind, who won for his book on black holes. KC Cole, our moderator, managed to keep this herd of cats on the straight and narrow by having each of us answer her questions about science in general with our own particular examples from out books on black holes, the sense of smell, and E. coli.

The questions from the audience were fabulous. One person got up and said she had a two-part question. She wanted me to talk about the long-term evolution experiments Richard Lenski runs with E. coli, and she wanted Susskind to talk about whether the anthropic principle and the multiverse theory were compatible. One person. Incidentally, I answered first, prefacing my remarks by saying I think I got the easier question. When I was done, Susskind looked at me and said, “No, I got the easier question. Yes.”

You can read more about the event over at the LA Times book blog, but you won’t read much about multiverse theories or evolution experiments, or much of anything of substance, I’m afraid. Plus, I’m pretty sure no one’s ever called me a curmudgeon.

Later this week I’m heading out to Los Angeles for the book festival. I’ll be part of a panel Saturday morning at 10:30 on science books, moderated by KC Cole. My fellow panelists, Avery Gilbert and Leonard Susskind, are also among my fellow finalists for the Los Angeles Times Science Book Prize, which will be announced Friday night. So it’s possible that if you come see the panel the next day, one of us will have a particularly big smile on our face.

Microcosm will be coming out in paperback in July, but the new cover is already posted online. I like the design very much, although I must admit I’m crossing my fingers that in a couple weeks we’ll need to make a last-minute change…

In Microcosm, I write about how E. coli communicate with each other (and can eavesdrop on us). Here’s a great talk by Bonnie Bassler from Princeton on her pioneering work on microbial conversations, and why they’re so important to the rest of life on Earth.

Over on bloggingheads, I talk with Rob Carlson, one of the most perceptive thinkers around when it comes to pondering where biotechnology is headed. Until his new book comes out in the fall, this will have to tide us over….

In connection with my recent lecture on life, I had a good interview with the local NPR station in Oklahoma. We talked about making life from scratch, Microcosm, and the microbes that are eavesdropping on you from the inside. You can listen to it on this embedded player below, or download it from the KWGS web site.

Last year I took part in a talk about biology, terrorism, and art during the World Science Festival. One of the best things about the experience was getting to talk with people before and after the actual event. The crowd was loaded with artists (for example, the wonderful photographer Justine Cooper) giving serious, interesting thought to how we think about science, and how science changes how we think about the natural world.

I also met Richard Pell, who is trying to reinvent the natural history museum. It’s high time someone did. Natural history museums were originally developed to house a representative sample of the diversity of life. Yet for at least the past 10,000 years, people have been producing artificial diversity–strains of corn and horses and yogurt cultures that did not previously exist. In recent decades, as I explain in my book Microcosm, genetic engineering and synthetic biology has allowed scientists to make deeper changes to living things. But no one to my knowledge has been trying to organize this biotechnological history. Where is the first microbe to be patented? The first genetically modified tomato to be introduced into a farmer’s field? Whether you embrace synthetic biology or think that it desecrates nature, the fact remains that it’s part of our physical and cultural landscape. It needs to be chronicled as much as dinosaurs and oysters do.

Pell recently emailed me to point me to a web site where people can learn more about his project, which he called the Center for PostNatural History. Check it out.

I’m honored to report that I’ve been asked to deliver this year’s John Wesley Powell Memorial Lecture.

Here is a description of the lecture series from its organizers, the Southwestern and Rocky Mountain Division of the American Association for the Advancement of Science:

The John Wesley Powell Memorial Lectures were inaugurated in 1929 in honor of the distinguished geologist and leader of the first expedition down the Colorado River through the Grand Canyon. Each year since then, with the exception of the years during WWII when the Division did not hold meetings, SWARM has invited a distinguished scholar to deliver a lecture at the Annual Meeting on a subject of his or her choosing. An attempt has always been made to select speakers who represent as wide a diversity of scientific endeavor as possible. Some of the previous Powell lecturers have included Oliver Sacks (2000), Holmes Rolston III (1998), Carl Sagan (1992), Lawrence Slobodkin (1987), Paul S. Martin (1978), Eugene Odum (1968), A.H. Compton (1939), Otto Struve (1934) and Aldo Leopold (1933).

The title of my lecture will be, “What Is Life? An Ancient Question Meets Twenty-First Century Science.” I’ll be delivering my lecture on the evening of March 29,  during AAAS-SWARM’s annual meeting. It will take place at the Allen Chapman Activity Center at the University of Tulsa in Tulsa, Oklahoma.

The talk is open to the public. More details can be found here.

I’m looking forward to visiting Oklahoma for the first time, and I hope readers in and around Tulsa will be able to join me.

[Image: Grand Canyon National Park]