A Blog by Robert Krulwich

Noah (and his ark) Updated, Improved for Our Time

Instead of the Noah you know, the one who built the ark, sheltered all those animals, sailed for 40 days and 40 nights and got to see God’s rainbow, instead of him, I want you to meet a new one. An updated version.

This Noah shows up in a tough little essay written by Amy Leach, of Bozeman, Montana, who knows her science, knows there’s a flood coming—a flood of humans, seven billion and counting, already swamping the Earth, crowding the land, emptying the sea, and her more modern Noah—informed, practical, not inclined to miracles—has a different plan. He announces,

water color painting with text reading ''unfortunately, animals. we are not going to be able to bring all of you with us this time.''
Illustration by Robert Krulwich

The old Noah, you may remember, squeezed eight humans (wife, kids, their spouses) and at least two of every critter, big and small, onto his crowded ship. But the new Noah, being more practical, feels he can winnow a little. “Everybody” is a lot of animals, more than you know. Back in the day, Amy Leach writes,

pink watercolor background with two drawings of frogs peeking up over the text, which talks about what it would be like to bring two of every creature onto noah's ark
Illustration by Robert Krulwich

And, honestly, (I’m thinking to myself), if the world lost a scorpion or two, would anyone notice? Or want them back? And blotchy toads, biting little flies—some animals are hard to keep going on a tight, crowded ship. On the last voyage, dormitory assignments were beyond difficult.

And all those supplies? Amy Leach writes how the first Noah would have had …

a yellow watercolor background covered with text about collecting food for animals
Illustration by Robert Krulwich

This doesn’t mean we don’t care, new Noah says to the animals. We definitely, absolutely want to bring a bunch of you with us. But, we’ve got to be practical.

Even if our ark has grown to the size of a planet, carrying everybody through is not going to be logistically possible, which is why, he says,

blue watercolor background with black text on it about being in charge of a future noahs ark where not all animals are included
Illustration by Robert Krulwich

And anyway, that first Noah? He lived in a different age, a time they call the Holocene, before humans began to dominate and crowd out the other species. Back then, there weren’t as many people. And there were more kinds of animals, closer by, hiding in the woods, clucking in the yard, so the world was more various then, more intimate, more riotous, and thinking about it (a little wistfully, if only for a moment), the new Noah quietly recalls that on that first ark …

yellow watercolor background with text on top related to how noahs ark would be different today than it was in the Old Testament
Illustration by Robert Krulwich

And now, animals, it’s time for many of you to step away. You’ve had your unruly eons. They were wild, unplanned, noisy, great fun. Natural selection ran the world. Crazy things happened. Those were good times, Amy’s essay concludes …

blue watercoor with black text on top that reads''But the future belongs to us.''
Illustration by Robert Krulwich

Amy Leach is a writer living in Bozeman. Her collection of very short pieces—about jellyfish, beaver, salmon, plants that go topsy turvy and stand on their heads—are collected in a wonderful little book called “Things That Are.” In this column I do to Amy what the new Noah is doing to our planet: I edited her down, sliced, diced, slimmed (lovingly, I hope), trying to give you a taste for her fierce, crazy prose. But like the planet, she’s wilder in the original, so I hope you go there and sample the unedited version.

A Blog by Carl Zimmer

Life Under A Faint Sun

If you could have looked up at the sky 4 billion years ago, you would have seen a sun much dimmer than ours today. And if you looked down at the Earth’s oceans, you would have seen an expanse of bobbing waves.

That’s a problem–a simple one, but a big one. And scientists have been wrestling with it for fifty years.

The brightness of the sun over the past 4.5 billion years. From Feulner 2011 http://arxiv.org/abs/1204.4449

The evidence for these two facts about the early Earth–a dim sun and liquid oceans–were already strong in the 1960s. Astronomers have compared our sun today to other stars of different sizes and ages, and they’ve been able to reconstruct much of its history. The sun started out about 70% as bright as today. It slowly grew brighter; even two billion years ago (2.5 billion years after the Earth formed), the sun was still just 85% as bright as today.

On its own, the faint young sun could not have kept the Earth from freezing over. And yet there are lots of signs in ancient rocks that the Earth was wet. Tiny crystals dating back over 4 billion years have a chemistry that required liquid water. Ancient rocks known as pillow lavas must have formed as molten Earth oozed out into sea water.

As early as the mid-1960s [pdf], scientists realized that these two lines of evidence posed a paradox: what is now known as the Faint Young Sun Paradox. It was a serious problem that required serious thought. It didn’t just mean that the evidence from geology and astronomy wasn’t meshing together. It also added a puzzle to the rise of life on Earth. Life would have had a hard time getting started on a planet of ice.

In 1972, Carl Sagan and his colleague at Cornell George Mullen proposed a solution to the paradox: the greenhouse effect. When radiation from the sun hits the Earth, some of it bounces back into space, but some of it lingers, thanks to heat-trapping gases in the atmosphere. The early Earth would have released gasses from its rocks, creating the first atmosphere. If it had the right chemistry, Sagan and Mullen argued, it might have been able to keep the Earth warm enough to melt ice. They suggested ammonia as a plausible heat-trapper on the young planet.

Unfortunately, ammonia turned out to be a bad solution. Other scientists figured out that ultraviolet rays from the sun would have destroyed any built up ammonia in the atmosphere in less than a decade. That’s not much of a defense against the deep freeze.

But ammonia is not the only greenhouse gas in the game. Today, carbon dioxide and methane are two important molecules keeping our planet warm (and warmer). Scientists have tried for years to narrow down the possible range of the two gases on the early Earth. It’s a very tricky puzzle, because scientists know that there are many factors that can influence their concentrations. And there were factors on the early Earth that we don’t experience today, such as a fairly steady bombardment of comets and giant meteors. Making matters even more complicated, greenhouse gases are not always greenhouse gases. Once the proportion of methane to carbon dioxide gets too high, it produces an organic haze that bounces radiation back into space, cooling the planet.

The consensus today is that methane and carbon dioxide may have warmed the early Earth a fair amount, but not enough to solve the paradox. So scientists are looking at other possible factors. Clouds may have helped. The early Earth rotated quickly through a 14 hour day, which may have changed how the oceans circulated–and thus how they trapped heat. But wide scope still remains for more ideas.

Today in Science, Robin Wordsworth and Raymond Pierrehumbert of the University of Chicago offer two new players to the Faint Young Sun game. They argue that a pair of molecules that have hitherto been neglected–hydrogen (H2) and nitrogen (N2)–could have made up a lot of the difference between the sun’s feeble glow and the Earth’s life-sustaining warmth.

There’s hardly any molecular hydrogen in our atmosphere today, because it easily skips out of the atmosphere into space. But Wordsworth and Pierrehumbert argue that such an escape would have been much harder for hydrogen on the early Earth, partly because it couldn’t get as big of a boost from ultraviolet rays from the sun. They estimate that hydrogen could have made up as much as thirty percent of the atmosphere. They also argue that nitrogen levels were three times higher than today.

On their own, nitrogen and hydrogen don’t do a very good job of trapping the sun’s heat. But when they crash into each other, their structure briefly changes, allowing them to absorb radiation. Wordsworth and Pierrehumbert built a model of a hydrogen and nitrogen-rich early atmosphere and found that as the molecules crashed into each other, they soaked up a lot of heat–enough, they argue, to heat the planet 10 to 15 degrees centigrade. That would go a long way to resolving the Faint Young Sun Paradox.

This new study probably won’t bring the fifty-year debate to a halt. In an accompanying commentary, James Kasting at Penn State argues that nitrogen is too heavy to absorb much radiation, even in the midst of a collision. Instead, Wordsworth and Pierrehumbert are stocking the cabinet that aspiring chefs can raid when they are trying to come up with new recipes for the early Earth.

If hydrogen and nitrogen do turn out to be part of the answer to the Faint Young Sun Paradox, they may have some fascinating implications about life on Earth–and elsewhere. Molecular hydrogen is fine dining for certain types of microbes known as methanogens. As soon as they evolved, they would have been able to feast on a sky full of hydrogen. By devouring the Earth’s protective hydrogen, they might have cooled the planet until it experienced its first glaciers. And beyond Earth, we may need to expand our concept of what kind of planet could support life. If they turn out to have a rich supply of hydrogen and nitrogen, they may offer a toasty incubator for aliens.

Image: “The ‘Fighting Temeraire’ Tugged to her Last Berth to be Broken up” by William Turner, via Wiki-Paintings

A Blog by Carl Zimmer

Life with a capital L? (Like Zimmer with a capital Z?)

Over on Facebook, David Hillis, an evolutionary biologist at the University of Texas, took up my question as to whether anyone can define life in three words. His short answer was no, but his long answer, which I’ve stitched together here from a series of comments he wrote, was very interesting (links are mine):

Like all historical entities (including other biological taxa), it is only sensible to “define” Life ostensively (by pointing to it, noting when and where it began, and following its lineages from there) rather than intensionally (using a list of characteristics). This applies to the taxon we call Life (hence capitalized, as a formal name). You could define a class concept called life (not a formal taxon), but then that concept would clearly differ from person to person (whereas it is much less problematic to note examples of the taxon Life). So, I’d say that I can point to and circumscribe Life, and that it the appropriate way to “define” any biological taxon. A list of its unique characteristics is then a diagnosis, rather than a definition. So, I’d argue that any intensional definition of Life is illogical (does not recognize the nature of Life), no matter how many words are used.

Defining Life (the taxon) is like defining other particular historical entities. We don’t “define” Carl Zimmer or the United States of America by listing out their attributes. Instead, we point to their origin and history. The same should be true for Life. If we ever discover a Life2, we’ll have a new origin and history to point to.

The question people actually want to ask is “Are there entities in the universe that are similar to the Life we know about here on Earth?” The answer, of course, depends on what people mean by the arbitrary meaning of “similar”. One person might answer “I mean ‘self-replicating with variations’.” Then, the answer is yes: humans have created imperfectly self-replicating systems (“artificial life”) here on Earth. But then someone else says “But that is not what I meant by similar…I meant that they had to have metabolism and cellular structure and a nucelic-acid-based genetic system.” OK, then we have to keep looking to find something that similar. But then someone else says “But that’s pretty arbitrary…I’d still consider it alive if it didn’t have cellular structure.” Exactly…it is indeed arbitrary to argue over how similar something has to be to consider it “similar” to Life. So, in the end, we can ostensively define Life (by referencing its origin and history), and we can do the same for other historical entities that some people might also want to say are alive, but there can be no simple “right” answer that will satisfy everyone about which entities should be considered alive, because we all emphasize different characteristics in defining an arbitrary class concept of “life”.

A Blog by Carl Zimmer

Can you define life in three words?

We are all sure we know what life is, but if you try to actually define it, things get tricky fast. I wrote a feature about the scientific struggle to define life in 2007 for Seed, and I’ve been keeping tabs on the evolution of this metaphysical quandary ever since. I was particularly intrigued to discover recently that one scientist thinks he can define life–and do so in just three words. I’ve written an essay about his short and sweet definition for the web magazine Txchnologist. Check it out.

A Blog by Carl Zimmer

Arsenic life and all that: My new book review for the Wall Street Journal

The Wall Street Journal recently asked me to review a new book called First Contact: Scientific Breakthroughs in the Hunt for Life Beyond Earth. Astrobiology is a tricky subject to write about these days. It’s intensely exciting, despite the fact that its main object of study–life on other planets–has yet to be discovered.

I’ve given some thought to how we journalists should cover such a paradoxical science. We shouldn’t dismiss it outright, because astrobiologists have discovered fascinating things about life here on Earth, even if they have yet to find aliens. Yet we shouldn’t feel obligated to pump up every claim about the possibility of life elsewhere. We should be content to paint a portrait of the scientific process–including the intense debates–in all its gorey detail.

By this measure, I don’t think First Contact works. The author, Marc Kaufman, declares at the outset of the book that “before the end of this century, and perhaps much sooner than that, scientists will determine that life exists elsewhere in the universe.” Not whether life exists, mind you, but that it exists.

I don’t think he backed up that bold claim. Instead, he pumps up intriguing, but inconclusive, evidence. He portrays the scientists who made claims for arsenic life, for example, as bold, out-of-the-box thinkers, and criticisms as little more than the rants of bloggers. He’s not alone–on Thursday, Time picked a member of the arsenic life team as one of their 100 most influential people of 2011. But these portrayals don’t match the reality of the arsenic life saga. I find the manufactured dichotomy between the supposed mavericks and the mean-spirited critics to be particularly off target. Remember, a lot of the critics of arsenic life are astrobiologists themselves.

For a better example of how to embrace scientific debate, check out Richard Panek’s The 4 Percent Universe: Dark Matter, Dark Energy, and the Race to Discover the Rest of Reality which I reviewed for the Washington Post in January. Panek doesn’t shy away from the intense competition and bad-mouthing that cosmologists engaged in as they rushed to establish the deep mystery of the universe. It’s a rich story that doesn’t shy away from the messiness and uncertainty that the big questions in science inevitably create.

A Blog by Carl Zimmer

Of arsenic and aliens: What the critics said

A lot of people are interested in my Slate story yesterday on the arsenic aliens. It’s still the most-read story of the site at the moment, Slashdot and others have linked to it, and I’m doing some more radio and maybe other media (details to come).

I think that what has gotten so much attention to the story is just how many scientists had such critical things to say. The verdict was not unanimous, but the majority was large. I was only able to quote a tiny bit from just a few of the scientists I communicated with, so I thought, for those who’d like to delve more deeply into this, that I’d post a list of everyone I spoke to, and, when possible, post their reactions. A lot of scientists replied to me by email or even attached word files where they went on at length. I put together a similar dossier for another biological controversy–the search for soft tissue in dinosaur fossils–and I think (or at least hope) that this sort of exercise can help further discussion.

Of course, as I and others have reported, the authors of the new paper claim that all this is entirely inappropriate. They say this conversation should all be limited to peer-reviewed journals. I don’t agree. These were all on-the-record comments from experts who read the paper, which I solicited for a news article. So they’re legit in every sense of the word. Who knows–they might even help inform peer-reviewed science that comes out later on.

I’m going to post everything under the fold here, but it will take a little while. I’ll just re-save the post every time I add a new one, and I should be done before too long. So keep refreshing, or just drop by again later…

PS–Science has made the paper at the center of this controversy free. Get it here.

(more…)

A Blog by Carl Zimmer

And the skeptics keep chiming in…George Cody on arsenic life

One of the challenges of writing on deadline is that people are not waiting every moment of the day to answer your questions. My Slate piece on arsenic life was based on a dozen or so responses from an overwhelmingly skeptical group of experts. And now, an hour after my story went live, I got a reply from George Cody, a chemist at the Carnegie Institution who co-authored a major 2007 “weird life” report. Rather than let this thirteenth comment molder in my inbox, let me share it with you. It’s a bit technical but illuminating. I’ve condensed it for clarity (my clips marked by ellipses)–

I have been aware of the hypothesis of the possibility of substitution of arsenate for phosphate for some time…The issue that always comes up is the facility of hydrolysis of arseno ester bonds….The correct experiment to do would be mass spectrometry which would unambiguously determine whether an arsenate backbone was present or not in the DNA.  I cannot accept this claim until such an experiment (easily done) is performed. ..

I recall a summer intern in my laboratory accidently culturing up a bacterial biofilm from a solution of concentrated fumarate, urea, and ammonium hydroxide in ultra-pure water (not surprisingly ammonia oxidizing bacteria); we were surprised but evidently the microorganisms were able to obtain the necessary nutrients, e.g. phosphate, from somewhere to grow to a point be being readily observed.  Microorganisms can do quite a bit with a little.  I recall a report in Nature by Benjamin Van Mooy (WHOI) where it was shown that certain marine organisms could use sulfate in their lipids when the availability of phosphate is very low.  Actually, if arsenate had substituted for phosphate anywhere, I would have looked at the lipids first, again using mass-spectrometry.

Philosophically, if it turned out that an organism could use arsenate in place of phosphate, this would not in my opinion rewrite the rules of life as we know it; aside from the hydrolysis issue, arsenate is chemically very similar to phosphate.  A careful chemist could likely synthesize DNA oligomers with an arsenate backbone.  As I understand it this is precisely why arsenate is a poison.  Ultimately, the idea of a shadow biosphere is interesting, but it would have to be demonstrated to be truly distinct from extant biochemistry, e.g. truly novel metabolic pathways, different bases for coding, different amino-acids or better still enzymes that were not based on amino-acids at all.

As the old adage goes “Extraordinary claims require…”

Likely what I have said mirrors what you have heard from others.

Indeed, it has.

A Blog by Carl Zimmer

Of Arsenic and Aliens

LakeMonoRumors have been swirling this week about a press conference NASA is starting right now. Some people have speculated that they’re going to announce evidence for life on another planet.

Well, not quite. Scientists have found a form of life that they claim bends the rules for life as we know it. But they didn’t need to go to another planet to find it. They just had to go to California.

The search for alien life has long been plagued by a philosophical question: what is life? Why is this so vexing? Well, let’s say that you’re hunting for change under your couch so that your four-year-old son can buy an ice cream cone from a truck that’s pulled up outside your house. Your son offers to help.

“What is change?” he asks.

“It’s…” You trail off, realizing that you’re about to get into a full-blown discussion of economics with a sugar-crazed four-year-old. So, instead, you open up your hand and show him a penny, a nickel, a dime. “It’s things like this.”

“Oh–okay!” your son says. He digs away happily. The two of you find lots of interesting things–paper clips, doll shoes, some sort of cracker–which you set aside in a little pile. But you’ve only found seventeen cents in change when the ice cream truck pulls away. Tears ensue.

As you’re tossing the pile of debris into the trash, you notice that there’s a dollar bill in the mix.

“Did you find this?” you ask.

“Yes,” your son sobs.

“Well, why didn’t you tell me?”

“It’s not change. Change is metal. That’s paper.”

Scientists have proposed hundreds of definitions for life, none of which has emerged as the winner. (For more on this quest, see “The Meaning of Life,” a cover story I wrote for SEED.) NASA, which would like to find life elsewhere in the universe, has taken a very practical approach to the question, simply asking what sort of definition of life should would be the best guide for their search. Traditionally, they’ve put a priority on life as we know it. All life on Earth uses DNA or RNA to encode genes; all life on Earth uses the same basic genetic code to translate genes into proteins; all life uses water as a solvent. One reason that NASA has put so much emphasis on looking for life on Mars is that it’s plausible that life as we know it might have existed on Mars back when the planet was warm and watery. And besides, how are we supposed to look for a form of life we’ve never seen before?

But in 2007 a National Academies of Science panel urged that we take a broader view of life, so that we wouldn’t miss the dollar bill in the couch. Other kinds of life were at least imaginable–such as organisms that used different backbones for their genes, or perhaps might swim through liquid methane like fish swim in water. (Here’s my write-up in the Times.) Some of the panelists–most notably, Steven Benner of the Foundation for Appllied Molecular Evolution–even endorsed a more radical notion. As I described in this feature for Discover, Benner and others speculate that maybe alien life is here on Earth.

A lot of evidence, for example, suggests that the first forms of life used RNA as both genes and enzymes. Later, double-stranded DNA evolved and DNA-based life wiped out RNA life. But perhaps RNA life still clings to existence in places where DNA-based life can’t drive them extinct. Benner suggests tiny pores in rocks that would be too small for bacteria.

No one has found RNA life yet, nor have they found any all-natural alien on Earth. But as I point out in Microcosm, there are definitely aliens among us.

They’re called E. coli.

Or, rather, they are laboratory stocks of E. coli that scientists have transformed so that they use new genetic codes or even use new nucleotides, the “letters” of DNA. No life that we know of has ever lived this way.

NASA’s press conference concerns another nearly-alien kind of life on our own planet. NASA has sponsored many expeditions to the toughest places on Earth for life to survive, from glaciers to deserts to acid-drenched mines. One of these expeditions was to Mono Lake, a practically toxic body of water, an extreme environment. It’s very salty, very alkaline, and is steeped in arsenic. The “weird life” report singled out arsenic-based life as one topic worth investigating, so Felisa Wolfe-Simon of the NASA Astrobiology Institute and her colleagues isolated a strain of bacteria and brought it back to the lab to study its growth.

As I mentioned earlier, life as we know it uses DNA for its genes (except for some viruses that use RNA). DNA has a backbone made of two alternating units: sugar and phosphate. Phosphate is one phosphorus atom and four oxygen atoms. It just so happens that arsenic–despite being a poison–has a lot of chemical properties similar to phosophorus. In fact, one arsenic atom and four oxygen atoms combine to form a molecule called aresenate that behaves a lot like phosphate.

Wolfe-Simon and her colleagues reared the bacteria in their lab, initially feeding them a typical diet of essential nutrients, including phosphate. But then they gradually reduced the phosphate in their diet and replaced it with arsenate. Before long, as they report today in Science, the bacteria were growing nicely on an all-arsenate diet, without a speck of added phosphate. The scientists then probed the DNA of the bacteria and concluded that they were sticking the arsenate into the DNA in place of phosphate. Phosphate is also vital for other molecules, such as proteins, and the scientists found arsenate in them as well. In other words–arsenic-based life.

Or…maybe not. In Science, reporter Elizabeth Pennisi writes that some scientists are skeptical, seeing other explanations for the results. One possible alternative is that the bacteria are actually stuffing away the arsenic in shielded bubbles in huge amounts.

I got in touch with Benner, who also proved to be a skeptic. “I do not see any simple explanation for the reported results that is broadly consistent with other information well known to chemistry,” he says. He pointed out that phosphate compounds are incredibly durable in water, but arsenate compounds fall apart quickly. It was possible that arsenate was being stabilized by yet another molecule, but that was just speculation. Benner didn’t dismiss the experiment out of hand, though, saying that it would be straightforward to do more tests on the alleged arsenic-DNA molecules to see if that’s what they really are. “The result will have sweeping consequences,” he said.

If Wolfe-Simon can satisfy the critics, this will be research to watch. The Mono Lake bacteria probably don’t actually exist in an arsenic-based form in nature, since they grow much faster on phosophorus. They’re aliens, but aliens in the same way unnatural E. coli are, thanks to our intervention. But Wolfe-Simon’s results suggest that life based on arsenic is at least possible. It might even exist naturally in places on Earth where arsenic levels are very high and phosphorus is very scarce.

Such a discovery would indeed be huge news–although not as huge as a similar discovery on another planet. For now, we will have to content ourselves with arsenic-laced dreams.

(PS: You should be able to watch the press conference live starting at 2pm Thursday 12/2 here.)

Reference: Wolfe-Simon et al, “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus” Science, 10.1126/science.1197258

[Image of Mono Lake by .Bala via Flickr, under Creative Commons License]

[Update: Fixed Wolfe-Simon’s name. Now I am left with images of wolf salmon roaming in packs.]

[Update: Fellow Discover bloggers Ed Yong and Phil Plait are on the case, too.]

[Update: I’ve been adding in various corrections pointed out by astute readers. Importantly, the researchers raised the bacteria with no *added* phosphate. But the medium did have a little phosphate in it anyway. More about this on Monday!]

[Upate: Well, Monday became Tuesday, but better late than never: Here’s my new article on the arsenic backlash at Slate.]

A Blog by Carl Zimmer

The 2009 John Wesley Powell Memorial Lecture: "What Is Life?"

powell220.jpg 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]