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Paleontologists trying to trace human evolution can’t scrutinize a living Neandertal or Homo erectus. But scientists hoping to piece together how photosynthesis began might have that luxury. Microbiologists suspect that bacteria that preserve stages in photosynthetic evolution—call them missing links if you like—are still with us. No one has found such a microbe—yet.

Bacteria are the Thomas Edisons of metabolism. They have “invented” myriad biochemical pathways that enable them to eke out a living from substrates as diverse as the oils on your skin, the tiny amounts of carbon monoxide in the atmosphere, and the hydrogen sulfide spewed by deep-sea volcanic vents. That metabolic diversity might include photosynthetic intermediates, scientists argue.

Researchers hope that such microbes will help them determine how early cells assembled the photosynthetic machinery, which involves more than 100 proteins working in concert to absorb light and make sugars. One of the most contentious questions in the field, as discussed in a recent Origins essay, is the origin of the photosystems, the molecular clusters that contain chlorophyll and other light-capturing proteins. Photosystems come in two flavors, I and II. Plants, algae, and primitive cyanobacteria all have both photosystems—and need both to exploit light energy. But other bacteria have only one molecular cluster—what scientists think are the ancestors of photosystem I or photosystem II. Microbial missing links might shed light on how the ancestors of today’s cyanobacteria ended up with two photosystems.

So far, researchers haven’t pinned down any of these missing links. But they take heart from a 2007 paper by microbial physiologist Donald Bryant of Pennsylvania State University, University Park, and colleagues that identified a new solar-powered bacterium. The researchers discovered the bug through metagenomics, which entails searching for organisms’ unique DNA strands rather than the creatures themselves. The bacterium’s DNA was lurking in samples from the microbial mats that grow in hot springs in Yellowstone National Park.

Subsequently, the researchers reared the bug in the lab (left, two jars of the bacteria) and sequenced its

jars1.jpggenome. The bacterium isn’t photosynthetic. It has the “photo” part down, absorbing light energy with chlorophyll to make the ATP necessary for living. But it hasn't mastered “synthesis.” Instead of using carbon dioxide to manufacture sugars, it depends on other bacteria for its carbon needs.

What makes the microbe noteworthy is that it belongs to a group, the Acidobacteria, that researchers had thought didn’t have light-harvesting ability. By expanding the range of bacteria that can use light, the discovery implies that “photosynthesis is more widely distributed than previously thought,” Bryant says. That means bacteria with other unknown metabolic styles, including possible photosynthetic missing links, are probably waiting for the scientists who are now looking for them.

—Mitch Leslie

As described in this month's Origins essay, power-hungry bacteria devised a way to capture solar energy more than 3 billion years ago, and the world hasn’t been the same since. To find out more about the nitty-gritty of how photosynthesis works, you might scour the Internet—and be disappointed to learn that the major texts on the subject aren’t available free online.

But there are plenty of other places to feed your curiosity. To learn the basics, start with this article from Arizona State University, Tempe, or this backgrounder from Estrella Mountain Community College in Avondale, Arizona. A more technical tutorial from the University of Illinois, Urbana-Champaign, delves into the mechanics of photon absorption by the photosystems, where chlorophyll and other pigments that capture light reside.

The Web abounds with animations of the photosynthetic reactions—some enlightening and some reminiscent of filmstrips you might remember from junior high science class. Two sites stand out. Part of a set on cell biology, these animations from San Francisco-based biologist and artist John Kyrk render the molecular events of the so-called light reactions, which stash solar energy as chemical energy, and the dark reactions that manufacture carbohydrates. In this narrated animation from North Dakota State University in Fargo, you can follow along as proteins ferry electrons and pump hydrogen ions. A second animation from the same group explores photosystem II, one of the light-harvesting protein complexes in plants, algae, and cyanobacteria that probably evolved from simpler structures in bacteria.

For more sites, check this roundup from ASU and the University of Illinois. There you’ll find links to pages on everything from the discovery of the vital enzyme RuBisCO (shown below) rubisco.jpgto herbicides, many of which disrupt photosynthesis.

—Mitch Leslie

Image credit: PDB

March 20, 2009

Tuning Up Photosynthesis

Organisms started capturing the sun’s energy through photosynthesis more than 3 billion years ago, as described in this month's Origins essay (Science, 6 March 2009, p. 1286). So natural selection has had plenty of opportunities to tinker with the photosynthetic machinery. Is it time we took over, overhauling the process to boost plant growth? That might be our best option for continuing to improve crop yields, says plant scientist Stephen Long of the University of Illinois, Urbana-Champaign.

Over the centuries, humans have transformed our crop plants through careful crossing, and lately, through genetic engineering. We’ve increased the percentage of energy that crops channel into edible parts.  As a result, grain now accounts for about 60% of the above-ground mass of a wheat plant, nearly twice the percentage of wheat plants in the 1940s. We’ve also made crops better at capturing light. We’ve bred corn and rice plants on which the upper leaves are more upright, allowing leaves lower on the stem to get their share of solar energy.

Changes like these are a big reason that crop yields per hectare have soared, nearly doubling between the 1950s and the 1990s alone. But these avenues for improving plants are nearly exhausted, Long says. Rice plants like these being harvested in Texas (left) rice(2).jpgcan’t support much more grain. “You need some room for stems and leaves.”

So crop scientists are looking toward a variable they haven’t systematically tried to enhance: the efficiency of the photosynthetic reactions themselves. But with 148 proteins taking part, choosing where to start is daunting. To identify some promising targets, Long and colleagues performed what he calls “an unusual marriage of molecular biology, supercomputing, and agriculture.” The researchers used a supercomputer to solve equations that track all of the chemical reactions through which plants transform carbon dioxide into carbohydrates. The computer randomly raised or lowered the levels of certain enzymes and determined the effects on photosynthetic efficiency. The most productive variant from each round moved on to the next round for further tweaking and testing.

The researchers’ surprising conclusion, which they reported in the October 2007 issue of Plant Physiology, is that photosynthetic efficiency is nowhere near its peak. After 1500 rounds of virtual refinements, they had elevated plant output by 76%. Increasing the levels of just four enzymes accounted for much of the gain. This strategy doesn’t require re-engineering the enzymes’ structure, but adjusting only their abundance. Long and colleagues now hope to take what they learned onto the farm, using genetic engineering to revise enzyme levels in tobacco and soybeans.

—Mitch Leslie

For more information, see
S. P. Long et al., “Can Improvement in Photosynthesis Increase Crop Yields?Plant, Cell & Environment 29, 315 (2006).

Photo credit: USDA

March 13, 2009

Minding the Oxygen Gap


The origin of oxygen-producing photosynthesis was a major event in Earth's history, not least because it paved the way for air-breathing animals like us. Nailing down the timing of this innovation would help researchers clarify the evolution of bacterial metabolism and better understand how oxygen released by the early bugs transformed almost every habitat on Earth.

So far, though, researchers fall into two camps whose answers differ by hundreds of millions of years, as discussed in Science’s Origins essay this month. The first widely accepted geological evidence for significant amounts of atmospheric oxygen is the great oxidation event (GOE) of 2.4 billion years ago. For some researchers, that means bacteria didn’t begin releasing oxygen until a little before the GOE. But according to other researchers, some clues—such as ancient oil thought to be the remains of oxygen-making photosynthetic bacteria—suggest that microbes turned on the gas several hundred million to more than 1 billion years before the GOE.

It’s no surprise that this is a tough question to answer. The evidence—whether it’s embedded in ancient rocks or inscribed in the DNA of modern bacteria—is hard to find and difficult to read. But scientists who argue for an early start to oxygen-releasing photosynthesis have another hurdle to overcome: explaining why it took so long for oxygen to accumulate in the atmosphere. Researchers are mulling several competing hypotheses.

90306N_Photosynth Try to picture the world without photosynthesis. Obviously, you’d have to strip away the greenery. Not just the redwoods and sunflowers, but the humble algae and the light-capturing bacteria that nourish many of the world’s ecosystems. Gone, too, would be everything that depends on photosynthetic organisms, directly or indirectly, for sustenance—from leaf-munching beetles to meat-eating lions. Even corals, which play host to algal partners, would lose their main food source.

Given its importance in making and keeping Earth lush, photosynthesis ranks high on the top-10 list of evolutionary milestones. In Science's Origins essay this week, author Mitch Leslie describes how scientists are delving into ancient rocks and poring over DNA sequences to try to piece together how and when organisms first began to harness light’s energy.

Although most modern photosynthesizers make oxygen from water, the earliest solar-powered bacteria relied on different ingredients, perhaps hydrogen sulfide. Over time, the photosynthetic machinery became more sophisticated, eventually leading to the green, well-oxygenated world that surrounds us today. In the lab, some biochemists are recapitulating the chemical steps that led to this increased complexity. Other researchers are locked in debates over just when this transition happened, 2.4 billion years ago or much earlier. 

A recent Science essay suggested that symmetrically shaped hand axes are precursors to symbolic behavior because making one requires holding a mental image of the finished product in your head. Origins asked a modern knapper, Steven Goldstein, an undergraduate anthropology major at Stony Brook University in New York state, to describe his thoughts as he created a stone tool.


A hand ax is a teardrop-shaped stone tool that you make by flaking off pieces of stone from both sides or “faces” of a stone, forming a sharp cutting edge. For more than 2 million years, early humans produced various kinds of these cutting tools.

I’ve had a lifelong interest in archaeology, and to better understand the process of making chipped stone tools, I began teaching myself how to replicate them. I started with Oldowan tools and eventually moved up to Neolithic and New World materials. Here’s what I do, and what I think, while I make an Acheulean hand ax, which early humans created about 1 million years ago.

A large percentage of functional Paleolithic hand axes were probably made in advance of jobs such as meat processing and woodworking. To make my tool, I anticipate a need, consciously decide to prepare for it, and imagine the shape and size of the tool I will need. Early humans used a variety of stones, including (but not limited to) quartzites, volcanic rocks like obsidian, flint, chert, and shale. With little high-quality material locally available around Stony Brook, I’m restricted to what I can buy or exchange with other knappers from around the country. In this case, that means angular cobbles of a low-grade flint.

I select the flint cobble that is the closest in its natural shape to my desired final product. Having seen hand axes in museums, class lectures, and published reports, I can easily imagine their schematic shapes (though of course I can’t assume my perception is the same as an early hominin’s). I’ve also collected a few hard, fist-sized quartzite pebbles of different sizes to use as “hammerstones.” Sitting over a tarp out behind the Social and Behavioral Sciences building on campus, I get right to work. I pick up the heaviest hammerstone (which will generate the most force) and hit it fairly hard against the side of the cobble. There’s a loud crack: I’ve just successfully removed a large, broad flake. I do it again and again, moving along the edge created by the previous blow and forcefully taking off large flakes from the cobble. Most of the thinning and shaping of the tool occurs in this primary stage, and so it’s important to remove large flakes. This photo shows this early stage:


February 26, 2009

Is a Hand Ax Really a Hand Ax?


Long before humans painted caves or made colorful necklaces out of snail shells, they manufactured beautifully symmetrical, teardrop-shaped stone tools that archaeologists call hand axes, such as the ones shown at left from Atapuerca, Spain. At least, hand axes seem beautiful to us today, even if their exact function and meaning are a matter of debate. Most archaeologists think that hand axes, which begin showing up at archaeological sites about 1.7 million years ago, were used to cut plants and butcher animals. And many assume that making such a symmetrical object required a mental template and the ability to impose a predetermined form on a piece of stone. As I discuss in this month’s Origins essay in Science, these talents could be considered proxies for symbolic capacities. And some researchers—as I discuss in a Random Sample in this week’s issue of Science—have suggested that hand axes were also the result of Darwinian “sexual selection.” According to this controversial idea, a well-made hand ax was a sign that its maker, presumed to be a guy, had good genes and would be a suitable mate for any gal lucky enough to have him.

So hand axes have been considered to be handy tools, courting devices, and signs of symbolic smarts. But what if they were none of these things? Since the early 1990s, one archaeologist has argued that there is no evidence early humans actually intended to make hand axes. Iain Davidson, now a professor emeritus at the University of New England (UNE) in Armidale, Australia, contends that the hand ax might have been what was left over when toolmakers were done striking sharp flakes from a stone core.

Davidson first argued for what he calls the finished-artifact fallacy in 1993, together with UNE psychologist William Noble, and he has elaborated on the idea in more recent publications. I caught up with him late last year at Harvard University, where he is currently a visiting professor. Over a long and pleasant lunch in Harvard Square, he made it clear that he has not changed his mind on the issue.

For one thing, Davidson says, archaeologists tend to focus their studies on the most symmetrical hand axes, thus introducing a bias into their analyses. They see more patterning than really exists on average and then interpret that patterning as evidence that early humans intended to create tools that look that way. And because hand axes were probably made by striking flakes from a core with a second stone—indeed, the marks where the flakes were taken off are clearly visible on the hand ax—archaeologists are making unproven assumptions when they conclude that the hand ax rather than the flakes were the most important product, Davidson contends. At the 500,000-year-old site of Boxgrove in England, for example, where hundreds of hand axes have been found, there are also signs that the flakes taken from them were used as tools by early humans.

“I can imagine a situation at Boxgrove where [early humans] were walking around with a core, striking off flakes when they needed them, and then abandoning the core when it was no longer useful,” Davidson told me. As for why the core would have that characteristic teardrop shape, Davidson explained that it would be easier to hold in the hand if you only took flakes off of one end.

Davidson’s view is definitely a minority one. “The form of [hand axes] clearly reflects the intention of the toolmakers,” says archaeologist Dietrich Stout of University College London. But few archaeologists argue that the flakes could not also have been used as tools, and Davidson’s idea does appeal to some. Anthropologist April Nowell of the University of Victoria in Canada, who challenges the sexual-selection hypothesis, told me that she is “sympathetic” to Davidson’s notion. “People get hung up on the symmetrical form that some [hand axes] have,” Nowell said. “We have exaggerated what a typical hand ax looks like, and we don’t think about the less refined ones. There is a variation from tools that just look like cores to those that look like hand axes.”

—Michael Balter

About Iain Davidson

Excavations at Boxgrove

PHOTO CREDIT: José-Manuel Benito Álvarez

Lion_man_photo.jpgWhen the Chauvet Cave in southern France was discovered in 1994, it rocked the archaeological world, in part because its paintings of lions, horses, and rhinos were spectacularly sophisticated—and also because radiocarbon dating suggested that these artworks had been executed as early as 32,000 years ago, making them the oldest known cave paintings. (Because there is no agreed radiocarbon calibration curve for dates earlier than 26,000 years ago, all dates are given in uncalibrated "radiocarbon" years; actual calendar dates are probably several thousand years earlier. See Science, 15 September 2006, p. 1560.)

Yet while Chauvet's paintings are unparalleled for their age in skill and technique, they did not stand entirely alone in the prehistoric art world. Indeed, many prehistorians were not completely surprised at their discovery, because there were already numerous indications that modern humans in Europe were making art that early; since Chauvet's discovery, a number of subsequent finds have confirmed that conclusion.

Chauvet may shelter the earliest cave paintings (but see below), yet previous excavations in Europe had found sculptures at least as old. Beginning in the 1930s and continuing until quite recently, archaeologists working in the Swabian Jura region of Germany have uncovered more than 20 figurines skillfully carved from mammoth ivory, including a superb half-lion, half-man sculpture from Hohlenstein-Stadel (see photo at left). Once radiocarbon dating became available after the 1950s, researchers found that these figurines were between 30,000 and 36,000 years old. The most recent objects, including a carved bird and a horse, were found in Hohle Fels Cave and reported by Nicholas Conard of the University of Tübingen in 2003. They too are at least 30,000 years old.

February 12, 2009

Neandertal Artists?

Originsblog_neandertal.jpgDid Neandertals use symbols and create art? This is the subject of one of the biggest, longest, and most contentious debates in the history of archaeology. Today, most researchers would agree that there is not a simple "yes" or "no" answer. But they might not agree on much else—just one more reason why Neandertals, whose genome sequence was announced today, are so intriguing.

Clearly identifiable Neandertal bones (like the front skeleton at left) appear no later than 130,000 years ago, often together with relatively sophisticated stone tools. But for about 90,000 years after that, there is little evidence that Neandertals produced anything that might be called art. There is certainly no indication that they ever painted caves, such as the spectacularly decorated Chauvet and Lascaux caves in France or Altamira in Spain, although one never knows what discoveries the future might hold—and one maverick archaeologist, Robert Bednarik (whom we featured last week) argues that Chauvet might have been painted by Neandertals, a decidedly minority view.

On the other hand, some researchers have complained bitterly that many colleagues are too quick to use the apparent absence of evidence for Neandertal symbolism to deny them their full humanity. John Speth, an anthropologist at the University of Michigan, Ann Arbor, expressed this view in the ironic title he gave to a 2004 paper in the journal World Archaeology: "News flash: negative evidence convicts Neandertals of gross mental incompetence."

I want to be the rap version of Richard Dawkins.

baba2.jpg—Baba Brinkman lyric

What’s a fan of evolution to do this week when confronted with so many events celebrating Darwin’s 200th birthday? On Monday, for example, one could have been in London for a debate, hosted by our friendly rival Nature, on whether humans are still evolving. What about a London reading of Darwin-related poems by one of his relatives? It would fit with the art theme of this month’s Origins essay, but it wasn’t quite compelling enough, especially when an even more provocative event was taking place here in Cambridge, where Darwin studied. Welcome to the “Devil in Dover and the Rap Guide to Evolution,” a traveling road show sponsored by the British Council and organized by microbiologist Mark Pallen, the author of The Rough Guide to Evolution (and its related blog).

The rain and sleet, and lack of publicity, meant that only a few dozen people filled the cavernous Cambridge University lecture hall. The opening act featured American journalist Lauri Lebo, who covered the 2005 trial in Dover, Pennsylvania, in which parents sued to prevent the school board from forcing the teaching of intelligent design in science classes. Lebo has written a book about the trial, The Devil in Dover, and she and plaintiff Cyndi Sneath discussed how the case ignited a civil war within the small town, with some of the parents even being called atheists by neighbors despite being regular churchgoers. Perhaps Lebo’s most powerful reminiscences concerned how she tried throughout the trial to convince her father, a religious fundamentalist, that the school board was acting dishonorably.

No one had started clapping rhythmically yet, but it was still time to bring on the headline act: Baba Brinkman, a former English literature student and Canadian hip-hop artist whose major claim to fame is his rap take on The Canterbury Tales—hence the boast on his MySpace page that he’s the Geoffrey Chaucer of hip-hop. Lebo herself was anxious to hear the so-called lit-hop artist, noting, “Anyone who can work Australopithecus afarensis into a rap impresses me.”