Plants are constantly proving that there’s more to them than meets the eye. We’ve written here before about plants seeing, hearing, and feeling; now researchers have discovered that our not-so-simple green friends also use mathematics.

Publishing in the open access journal eLife, scientists describe how plants can calculate how much starch to store at night, so they can continue growing 24/7.

Plants feed themselves during the day using energy from the sun to convert carbon dioxide into sugars and starch. Once the sun has set, they must depend on a store of starch to prevent starvation.

Studying Arabidopsis plants, the researchers determined that during the night, mechanisms inside the leaf measure the size of the starch reserve and estimate the length of time until dawn. Information about time comes from an internal clock, similar to our own body clock. The size of the starch store is then divided by the length of time until dawn to set the correct rate of starch consumption, so that, by dawn, around 95% of starch is used up.

The team used mathematical modeling to investigate how such a division calculation can be carried out inside a plant. They believe that information about the size of the starch store and the time until dawn is encoded in the concentrations of two kinds of molecules (one called “S” for starch, and the other, “T” for time). If the S molecules stimulate starch consumption, while the T molecules prevent this from happening, then the rate of starch consumption is S divided by T.

“The capacity to perform arithmetic calculation is vital for plant growth and productivity,” says study co-author Alison Smith, of the John Innes Centre. “Understanding how plants continue to grow in the dark could help unlock new ways to boost crop yield.”

Just don’t expect our leafy friends to balance your checkbook for you…

Image: Roepers

The old saying “You are what you eat” takes on new significance in the most comprehensive analysis to date of early human teeth from Africa.

Prior to about 3.5 million years ago, early humans dined almost exclusively on leaves and fruits from trees, shrubs, and herbs—similar to modern-day gorillas and chimpanzees.   However, about 3.5 million years ago, early human species like Australopithecus afarensis and Kenyanthropus platyops began to also nosh on grasses, sedges, and succulents—or on animals that ate those plants.

Evidence of this significant dietary expansion is written in the chemical make-up of our ancestors’ teeth.  These findings are reported in a series of four papers published this week in the Proceedings of the National Academy of Sciences, by an international group of scientists spread over three continents.

“These papers present the most exhaustive isotope-based studies on early human diets to date,” says the Academy’s own Zeresenay Alemseged, Senior Curator and Chair of Anthropology, and co-author on two of the papers (available here and here). “Because feeding is the most important factor determining an organism’s physiology, behavior, and its interaction with the environment, these findings will give us new insight into the evolutionary mechanisms that shaped our evolution.”

Plants can be divided into three categories based on their method of photosynthesis: C3, C4, and CAM.  C3 plants (trees, shrubs, and herbs) can be chemically distinguished from C4/CAM plants (grasses, sedges, and succulents) because the latter incorporate higher amounts of the heavier isotope carbon-13 into their tissues.  When the plants are consumed, the isotopes become incorporated into the animal’s own tissues—including the enamel of developing teeth.  Even after millions of years, scientists can measure the relative amounts of carbon-13 in teeth enamel and infer the amount of C3 vs. C4/CAM plants in an animal’s diet.

“What we have is chemical information on what our ancestors ate, which in simpler terms is like a piece of food item stuck between their teeth and preserved for millions of years,” says Alemseged.

These papers represent the first time that scientists have analyzed carbon isotope data from all early human species for which significant samples exist: 175 specimens representing 11 species, ranging from 4.4 to 1.3 million years in age.  The results show that prior to 3.5 million years ago, early humans ate almost exclusively C3 plants.  But starting about 3.5 million years ago, early humans acquired the taste for C4/CAM plants as well, even though their environments seemed to be broadly similar to their ancestors’.  The later genus Homo, including modern-day Homo sapiens, continues the trend of eating a mixture of C3 and C4/CAM plants—in fact, people who enjoy mashed potatoes with corn are practicing a 3.5 million-year-old habit.

What the studies cannot reveal is the exact identity of the food, and whether it also included animals that ate C4/CAM plants (an equally valid way to acquire carbon-13).  Possible C4/CAM-derived meals include grass seeds and roots, sedge underground stems, termites, succulents, or even small game and scavenged carcasses.  In 2010, Alemseged and his research team published the earliest evidence for meat consumption using tools, dating back to 3.4 million years ago—an additional line of evidence showing a dietary shift in human evolution.

“The change in isotopic signal documented by the new studies, coupled with the evidence for meat-eating in Australopithecus afarensis from Dikika around 3.5 million years ago, suggests an expansion in the dietary adaptation of the species,” says Alemseged.

The authors of this week’s papers also sampled fossils of giraffes, horses, and monkeys from the same environments and saw no significant change in their carbon isotope values over time—suggesting that the unique dietary transformation of early humans did not apply to other mammals on the African savanna.  The question of what drove the transformation, however, remains unresolved.

Andrew Ng is Communications Manager at the California Academy of Sciences.

Images: National Museums of Kenya. Photos by Mike Hettwer, Yang Deming

Could an odd plant with a terrible name show us that “junk DNA” has value after all?

The carnivorous bladderwort plant, Utricularia gibba, is a lightweight in the genome game. It has about 80 million DNA base pairs. By comparison, its relatives the grape and tomato have about 490 and 780 million base pairs, respectively. (You and I have about 3.2 billion base pairs, but hey, we’re humans.)

Despite its small genome, the carnivorous bladderwort is a complicated plant. Disguised as a lovely flowering beauty, it actually traps organisms such as insects and small fish in a bladder-shaped trap on its water-soaked roots—for nourishment, of course. And while that’s exciting, a new study in Nature has scientists even more excited about the carnivorous plant.

“The big story is that only 3 percent of the bladderwort’s genetic material is so-called ‘junk’ DNA,” says study co-author Victor Albert. The human genome, in contrast, includes about 98% junk DNA. But what kind of “junk” are we talking about?

Junk in the Trunk

“When complete genomes were first being sequenced, it became clear that only a small fraction of the DNA could be assigned a specific function,” explains Brian Simison, curator and director of the Academy’s Center for Comparative Genomics. “The functional regions or genes are primarily those that produce proteins or ribosomes. It has been hypothesized that these vast regions of unknown function were the product of duplications followed by loss of function due to the accumulation of random mutations and/or the accumulation of exogenous DNA from viruses. The term ‘Junk DNA’ emerged from these hypotheses.

“However, research on junk DNA is shedding new insights into these regions,” Simison adds. Last fall, he spoke with Science Today correspondent Barbara Tannenbaum about the ENCODE project. Conducting a huge international effort to look more into the junk part of the human genome, researchers determined that 80% of our genome actually had some function.

Since that time, ENCODE has come under some scrutiny. “I think the ‘controversy’ is overblown,” Simison says. “ENCODE scientists presented a testable hypothesis and it should be pursued as such. My bet is that some junk DNA will, in fact, turn out to be useless baggage from historical genomic events while other bits will prove to be required for normal human functions.”

No Junk in the Trunk

If our junk DNA is worth having around, then why doesn’t a meat-eating plant like the bladderwort need it? “Based on the miniscule number of complete genomes sequenced, it is unusual that the genome of the carnivorous bladderwort is only 3% junk DNA,” Simison says. “It may reveal interesting information about the function and organization of genomes. However, the sample size of complete genomes is so incredibly tiny that junkless genomes may not be that uncommon.”

So what happened to the junk? “That is the big question. Did it get deleted or did the carnivorous bladderwort not have it to begin with?” Simison asks. “To answer this we need to understand more about the evolutionary history of genomes and, in particular, we need to know more about the genomes of this plant’s ancestors.”

The bladderwort’s lack of junk DNA only adds to the mystery. Scientists hope to learn more as additional organisms’ complete genomes are sequenced—and as more research is conducted on the function of junk DNA.

Image: Bruce Salmon/Wikipedia

Four amazing and passionate scientists discussed different aspects of our changing world—wildlife, drought, storms and the tree-ring record—at a press conference titled, “Did Climate Change Cause Superstorm Sandy?”

Remember, these are scientists, not politicians (see more in Andy Revkin’s New York Times blog). They need evidence to see causal effect between one event and another. And for these recent storms and weather patterns, there just isn’t enough evidence. Yet.

But are these researchers glad that these events are focusing Americans’ attention (including the President in his recent State of the Union address) on climate change? Most definitely. Yes.

Here’s what they do know. Climate change is affecting the probability of storms like Sandy and Nemo. There is evidence that in our warming world, severe storms will happen more frequently.

Researchers understand that global warming and other human-related activities are affecting where animals live, move and mate, and when plants bloom.

Scientists also know that temperature increase is one factor in drought. Texas temperatures have risen steeply in just the past 15 years and drought has increased.  And now Texans are talking about climate change, said John Nielsen-Gammon of Texas A&M University. The drought alone didn’t alarm them about climate change, but the decreased water supply has made people and politicians alike take notice.

And the speakers are hopeful and passionate that we’ll start doing something about these effects—reducing fuel emissions, restoring habitats, becoming more aware of climate change.

What do you know and feel? Share with us here.

Midwest drought image: cwwycoff1/Wikipedia

Even if there are a number of planets that could support tectonics, running water and the chemical cycles that are essential for life as we know it, it seems unlikely that any of them would look like Earth.

The reason? Plants.

A series of articles in the journal report that both vascular and non-vascular plants (mosses, liverworts, algae) shaped the surface of Earth, affecting the oceans and climate of our planet as they began to appear 470 million years ago.

Vascular plants defined the way water flowed on the Earth. One article describes the interplay of plant evolution and river formation. Scientific American offers a summation:

Before the era of plants, water ran over Earth’s landmasses in broad sheets, with no defined courses. Only when enough vegetation grew to break down rock into minerals and mud, and then hold that mud in place, did river banks form and begin to channel the water. The channeling led to periodic flooding that deposited sediment over broad areas, building up rich soil. The soil allowed trees to take root. Their woody debris fell into the rivers, creating logjams that rapidly created new channels and caused even more flooding, setting up a feedback loop that eventually supported forests and fertile plains.

Another article in Nature Geoscience examines how early non-vascular plants affected the planet dramatically—causing global cooling and mass extinction in the oceans. British researchers working in the lab and with computer simulations discovered that these first plants caused the weathering of calcium and magnesium ions from silicate rocks, such as granite, in a process that removed carbon dioxide from the atmosphere, forming new carbonate rocks in the ocean. This cooled global temperatures by around five degrees Celsius.

In addition, by weathering the nutrients from rocks, the first plants increased the quantities of both these nutrients going into the oceans, fuelling productivity there and causing organic carbon burial. This removed yet more carbon from the atmosphere, further cooling the climate by another two to three degrees Celsius. It could also have had a devastating impact on marine life, leading to a mass extinction that has puzzled scientists.

The effect of plants on our planet is profound, remarks Liam Dolan of Oxford University, a researcher on the non-vascular plant study.

For me the most important take-home message is that the invasion of the land by plants—a pivotal time in the history of the planet—brought about huge climate changes. Our discovery emphasizes that plants have a central regulatory role in the control of climate: they did yesterday, they do today and they certainly will in the future.

Image: Dog Walking Girl/Wikipedia

Presenting at the National Meeting of the American Chemical Society, MIT’s Daniel Nocera, PhD, announced the first practical artificial leaf.

“A practical artificial leaf has been one of the Holy Grails of science for decades,” said Dr. Nocera, who led the research team. “We believe we have done it. The artificial leaf shows particular promise as an inexpensive source of electricity for homes of the poor in developing countries. Our goal is to make each home its own power station,” he said. “One can envision villages in India and Africa not long from now purchasing an affordable basic power system based on this technology.”

About the shape of a poker card but thinner, the device is fashioned from silicon, electronics and catalysts, substances that accelerate chemical reactions that otherwise would not occur, or would run slowly. Placed in a single gallon of water in bright sunlight, the device could produce enough electricity to supply a house in a developing country with electricity for a day. It does so by splitting water into its two components, hydrogen and oxygen. These two gases would then be stored in an electricity-producing fuel cell located either on top of the house or beside it.

Right now, the artificial leaf is about 10 times more efficient at carrying out photosynthesis than a natural leaf. However, Nocera is optimistic that he can boost the efficiency of the artificial leaf much higher in the future.

And that’s not all. Science Now reports:

The new catalyst also appears highly stable. Nocera says his team has been operating the device for a week, using water from the nearby Charles River in Cambridge, without any drop in efficiency. The next step is to find out whether the device works equally well in seawater. If so, it could dramatically lower the cost of producing hydrogen fuel.

Use in the real world is not so far in the future, according to Discover’s 80beats blog:

Tata Group, an Indian conglomerate, plans on creating a power plant based on this research within the next year and a half.

“Nature is powered by photosynthesis, and I think that the future world will be powered by photosynthesis as well in the form of this artificial leaf,” said Nocera.

Deal me in!

Image courtesy of Wikimedia

If Termites Can Do It, Why Can’t We?
Lakshmi Reddi, an engineer at the University of Central Florida, believes that if termites can build soil towers that maintain a constant temperature of 85 degrees Fahrenheit, we should be able to design more energy efficient buildings. Similarly, he discussed the thermoregulating properties of animal and human skin—maintaining a constant temperature within our bodies despite outside temperatures. Just looking at a teeny part—the human fingertip—scientists are able to see how “the blood flows and adjusts velocity in response to ambient temperatures,” according to Reddi. He believes this can also be applied to more efficient and sustainable building design.

Adaptive Plants
Kon-Well Wang of the University of Michigan is working with biologists to learn from plants. Plant cells are remarkable at adapting and self-healing—basically morphing as their environment demands. The research is still very basic, but Wang believes his team could build structures that do the same thing—“designed to twist, bend, stiffen and even heal themselves,” from a press release. He sees potential applications in aircraft wings (morphing and flexible like bird wings) and morphing robots.

Hair-like Sensors
Chang Liu of Northwestern University is looking at biological hair sensors. Not the hair on your head, but the hair in your ears that helps you hear, the hair on the backs of cockroaches and on the legs of spiders that help them detect movement and the hair on fish that allow them to sense water flowing around them. Liu believes that he could build better, cheaper sensors for biomedical applications or underwater vehicles. More info on his research can be found here.

Bear Metabolic Suppression
Finally, researchers in Alaska made startling discoveries when observing black bears hibernate in a lab in Alaska. The bears’ heart rates slowed, their breathing reduced to one to two times per minute, their body temperature decreased only slightly and they lost no muscle or bone mass despite the fact they were asleep for five to six months on end. What if humans could hibernate like this? Craig Heller, one of the authors of the paper in Science told NPR:

…for people bedridden for long periods, or who are contemplating a long space voyage such as going to Mars and back, figuring out how to make a human more like a hibernating bear would have some advantages.

Image: Øivind Tøien/Institute of Arctic Biology/University of Alaska, Fairbanks

In a new study, published yesterday in the Proceedings of the National Academy of Sciences, researchers found that Neanderthals ate more than just meat. In addition, our ancient cousins cooked some of their foods, “suggesting an overall sophistication in Neanderthal dietary regimes,” according to the report.

Turns out that tooth tartar can tell a lot about a human species. By examining the calculus (that’s hardened plaque, not advanced mathematics) in dental remains of fossils from Belgian and Iraqi caves, the researchers recovered grains and phytoliths—evidence of plant-eating. (Neanderthals could’ve used some floss, eh?) Their diet was varied, according to the study :

Some of the plants are typical of recent modern human diets, including date palms (Phoenix spp.), legumes, and grass seeds (Triticeae), whereas others are known to be edible but are not heavily used today.

It appears Neanderthals cooked a good percentage of their grains and vegetables, but getting an accurate picture is difficult. From Scientific American:

To better assess starch grains from the samples, the researchers tried cooking similar plant products and found that heating the starches for more than half an hour rendered them largely unidentifiable, and thus they would not have been categorizable in fossil form.

Pallab Ghosh wrote in the BBC News that previous “chemical analysis of their bones suggested they ate little or no vegetables,” and anthropologists often speculated that Neanderthals disappeared 30,000 years ago due to their limited meat diet. This new evidence can now put that theory to rest, according to the authors.

Image from We El/Wikipedia

When the days grow longer, temperatures begin to rise, and San Francisco Giants’ pitcher Tim Lincecum throws out the first pitch of the season, I know that spring has arrived in San Francisco. As new leaves appear and flowers begin to bloom, we are certain that winter has left us behind. It’s easy for us to know when spring is here, but what about the trees and flowers themselves? How do they know when to drop their leaves, and when to bloom?

Scientists believe they’ve discovered a special molecule in plants that gives them the remarkable ability to “remember” winter and to bloom on schedule in the spring. Their results are reported in the December 2 issue of Science Express.

Sibum Sung, molecular biologist at the University of Texas and one of the paper’s authors, was searching for a mechanism that allows plants to recognize spring and – more importantly – distinguish between spring and a brief warm spell during winter. The key, Sung found, was the plants’ ability to remember that winter had passed.

“Plants can’t literally remember, of course, because they don’t have brains,” says Sung. “But they do have a cellular memory of winter, and our research provides details of how this process works.”

The process Sung referred to is called “vernalization.” It allows a plant to properly come out of hibernation during winter so that it can bloom. But experts have never really understood the genetic basis for how vernalization worked.

Until now. Sung and his co-author Jae Bok Heo dug deep into the DNA of arabidopsis, a small flowering plant related to mustard and cabbage. As they scoured the lines of genetic code, they discovered that arabidopsis’ DNA coded for a molecule they called COLDAIR.

The authors’ experiments revealed that while the plant hunkers down for the winter, COLDAIR is switched off. After 20 days of consistent freezing temperatures, COLDAIR gets switched on. This begins the 10 to 20 day process of preparing the plant for spring. Once complete, the plant is ready for warm temperatures, and other pieces of genetic code help the plant to bloom.

As many of us know, this system isn’t perfect. Sometimes flowers do bloom early, and they pay the price when temperatures quickly return to freezing. But over millions of years of evolution, COLDAIR has helped create a kind of “memory” in generations of plants, telling them when there’s been at least a month of cold and that spring might be just around the corner.

Of course, many questions remain. Sung admits they still don’t have the other pieces of the puzzle, like how does the plant know it’s been at least 20 days of cold temperatures? “That is one of the next questions we have,” he says. “How do plants literally sense the cold?”

The particular mechanisms require further study, but as long as COLDAIR keeps working, flowers will give us one more sign when spring has sprung.

Anne Holden, a docent at the California Academy of Sciences, is a PhD trained genetic anthropologist and science writer living in San Francisco.

Image by Roepers/Wikimedia

A species’ survival often depends on how skillfully they can beat out another species for food or other resources. But sometimes, a species’ survival depends on how well they work with their neighbor. If each organism helps the other, they can both flourish. This process, called “symbiosis,” explains why bacteria thrive in our guts (because we thrive with them), how sharks don’t seem to mind the so-called “cleaner fish” that dart in and out of their mouths, and how delicate coral reefs can grow to the size of a small continent.

There are thousands of examples of symbiotic relationships on planet Earth. But has this practice always existed? In a study published last week, scientists uncovered evidence of a symbiotic relationship that existed over 470 million years ago. A relationship that paved the way for nearly every land organism on Earth.

In the November 2 issue of Nature Communications, a research team from the Royal Botanic Gardens and the University of Sydney pieced together earlier days of complex life by studying one of the most ancient land plants still in existence, the thalloid liverwort. Liverworts, often a nuisance in backyard gardens and greenhouses, have a small and flat ribbon-like structure.

Scientists have long suspected that the secret to the liverwort’s early success was a relationship with fungi living in the soil. But no one had been able to test it. Until now.

The team placed both liverwort and fungi in tightly controlled growth rooms to recreate Earth’s early days – hot and volatile. They found that when the fungi colonized the liverwort (a common fungal practice), the liverwort vastly improved its ability to take in carbon dioxide (CO₂). As a result, it grew and reproduced faster than if no fungi had been present. The fungi not only improved the liverwort’s ability to grow and reproduce, it helped the liverwort release substantial amounts of oxygen into the atmosphere. Something sorely lacking in Earth’s earliest days, and something for which we should all be thankful.

So what did the fungi get in return? They fed off the extra carbon the growing plants produced. In one experiment, the team found that just one liverwort plant could support fungi encompassing two tennis courts.

Professor David Beerling from the University of Sheffield, one of the authors of the study, was excited about how this research can help shed light on the earliest days of our planet. “By studying these ancient plants,” he says, “we open a window on the past to investigate how the earliest land plants evolved.”

Anne Holden, a docent at the California Academy of Sciences, is a PhD trained genetic anthropologist and science writer living in San Francisco.

Creative Commons image by Eric Guinther