David Suzuki, Air, and Intelligence

David Suzuki talking about air and alveoli
March 12, 2008 -- 11th Annual Commonwealth Lecture

Our lungs are made up of about 300 million capsules, or alveoli, and they are clustered around an alveolar stem like grapes. We have lots of these clusters in our lungs and we need them all to provide the surface area needed to come into contact with the air. If you flatten the alveoli of our lungs out into two dimensions, they would cover a tennis court. That is about how much surface area is wrinkled up in our lungs. Each alveolus is lined by a surfactant that reduces surface tension so that the air sticks to it. Immediately carbon dioxide rushes out of our bodies, oxygen and whatever else is in the air rushes in, and haemoglobin molecules in red blood cells grab on to the oxygen so that each beat of our heart can transfer that oxygen to every part of our bodies. And when you exhale you do not exhale all the air in your lungs. If you did that your lungs would collapse. About half of the air stays in your lungs even when you exhale.

The point I am trying to make is that you cannot draw a line that marks where the air ends and I begin. There is no line. The air is stuck to us and circulating through our bodies. We are air. It is a part of us and it is in us…

We think we are an intelligent creature, but what intelligent creature, knowing the role that air plays in our lives keeping us alive and connecting us to the past and into the future, would then proceed to use air as a garbage can and refuse to pay for putting carbon and all our pollutants into the atmosphere? We have much to reflect on the way that we use this sacred substance. It hurts me when I see young couples walking with a baby in a stroller and the baby’s nose is right at the level of the exhaust pipes of our cars. You might as well put a hose on the exhaust pipe and pump that stuff right into the baby’s body. Why are 15% of children in Canada now suffering with asthma? We are using the air as a toxic dump. We are air. Whatever we do to the air we do to ourselves.

Alex's Last Words

Excerpts from:
Brainy Parrot Dies, Emotive to the End
September 11, 2007 -- By Benedict Carey, The New York Times

He knew his colors and shapes, he learned more than 100 English words, and with his own brand of one-liners he established himself in television shows, scientific reports and news articles as perhaps the world’s most famous talking bird.

But last week Alex, an African gray parrot, died, apparently of natural causes, said Dr. Irene Pepperberg, a comparative psychologist at Brandeis University and Harvard who studied and worked with the parrot for most of his life and published reports of his progress in scientific journals. The parrot was 31.

Scientists have long debated whether any other species can develop the ability to learn human language. Alex’s language facility was, in some ways, more surprising than the feats of primates that have been taught American Sign Language, like Koko the gorilla, trained by Penny Patterson at the Gorilla Foundation/Koko.org in Woodside, Calif., or Washoe the chimpanzee, studied by R. Allen and Beatrice Gardner at the University of Nevada in the 1960s and 1970s.

In 1977, when Dr. Pepperberg, then a doctoral student in chemistry at Harvard, bought Alex from a pet store, scientists had little expectation that any bird could learn to communicate with humans, as opposed to just mimicking words and sounds. Research in other birds had been not promising.

But by using novel methods of teaching, Dr. Pepperberg prompted Alex to learn scores of words, which he could put into categories, and to count small numbers of items, as well as recognize colors and shapes.

“The work revolutionized the way we think of bird brains,” said Diana Reiss, a psychologist at Hunter College who works with dolphins and elephants. “That used to be a pejorative, but now we look at those brains — at least Alex’s — with some awe.”

Other scientists, while praising the research, cautioned against characterizing Alex’s abilities as human. The parrot learned to communicate in basic expressions — but he did not show the sort of logic and ability to generalize that children acquire at an early age, they said.

“There’s no evidence of recursive logic, and without that you can’t work with digital numbers or more complex human grammar,” said David Premack, emeritus professor of psychology at the University of Pennsylvania.

Dr. Pepperberg used an innovative approach to teach Alex. African grays are social birds, and quickly pick up some group dynamics. In experiments, Dr. Pepperberg would employ one trainer to, in effect, compete with Alex for a small reward, like a grape. Alex learned to ask for the grape by observing what the trainer was doing to get it; the researchers then worked with the bird to help shape the pronunciation of the words...

Even up through last week, Alex was working with Dr. Pepperberg on compound words and hard-to-pronounce words. As she put him into his cage for the night last Thursday, she recalled, Alex looked at her and said: “You be good, see you tomorrow. I love you.”

He was found dead in his cage the next morning, Dr. Pepperberg said.

Yangtze River Dolphin: Likely Extinct

Rare Yangtze River dolphin probably extinct: study
August 7, 2007 -- By Michael Kahn, Reuters

The long-threatened Yangtze River dolphin in China is probably extinct, according to an international team of researchers who said this would mark the first whale or dolphin to be wiped out due to human activity.

The freshwater dolphin, or baiji, was last spotted several years ago and an intensive six-week search in late 2006 failed to find any evidence that one of the rarest species on earth survives, said Samuel Turvey, a conservation biologist, at the Zoological Society of London, who took part in the search.

He said the dolphin's demise -- which resulted from overfishing, pollution and lack of intervention -- might serve as a cautionary tale and should spur governments and scientists to act to save other species verging on extinction.

"Ours is the first scientific study which didn't find any," he said in a telephone interview. "Even if there are a few left we can't find them and we can't do anything to stop their extinction."

The team, which published its findings in the Journal of the Royal Society Biology Letters on Wednesday, included researchers from the United States, Britain, Japan and China. The survey was also authorized by the Chinese government, Turvey said.

The last confirmed baiji sighting was 2002, although there have been a handful of unconfirmed sightings since then. The last baiji in captivity died in 2002, Turvey said.

During the six-week search, the team carried out both visual and acoustic surveys and used two boats to twice cover the dolphin's 1,669 kilometer range stretching from the city of Yichang just downstream from the Three Gorges dam to Shanghai.

The last such survey conducted from 1997 to 1999 turned up 13 of the mammals, but Turvey said fishing, pollution and boat traffic in the busy river, home to about 10 percent of the world's population, has likely meant the baiji's end.

"We covered the whole range of the dolphin twice," Turvey said. "It is difficult to see how we could miss any animals."

The dolphins will now be classified as critically endangered and possibly extinct but Turvey said there is little chance any remaining baiji are alive.

Researchers have known for years about the dolphin's precarious situation but indecision about how best to save the species meant little was actually done, he added.

This underscores the need to act quickly to prevent the extinction of other similar shallow-water aquatic mammals like the vaquita found in the Sea of Cortez and the Yangtze finless porpoise, Turvey said.

"One really needs to learn from this to make sure future conservation efforts are more dynamic," he said. "There has always been so much focus on 'save the whale' and 'prevent whaling' that it has led to these range-restricted shallow cetaceans slipping through the crack."

Genotypes, Phenotypes, Beavers, Birds and Fungi

Wild Neighbors: Requiem for the Hat Creek Beavers
July 17, 2007 -- By Joe Eaton, Berkeley Daily Planet

The week before the Fourth of July we were up at Lassen Volcanic National Park watching the traffic at Hat Lake. The place was jumping.

A male western tanager, resplendent in red and yellow, came down to the lake’s edge to drink. Audubon’s and Wilson’s warblers flashed in and out of the young lodgepole pines. A dipper made repeated shuttle flights from its nest below the highway bridge, alternately ducking underwater to forage or swimming like a little duck as it retrieved insects—mayflies?—from the lake’s surface. Another hard-working parent, a male white-headed woodpecker, commuted between its tree-cavity nest and some beetle-rich dead snag nearby. Tree swallows skimmed low over the lake, and noisy young spotted sandpipers chased each other around the beaver lodge.

No beavers, though. The last time we were there, we watched them late into the buggy twilight as they cruised the lake they had made, or at least augmented. This time the dam was in poor repair, and the lodge was surrounded by mud. We blamed that on the dry winter, but were still worried about the beavers. Later a ranger-naturalist told us they were gone. One had been found dead on the highway last year; another on a hiking trail—disease, old age, who knows.

Maybe another pair will wander up from the Warner Valley and take over the franchise. If not, the lake will inexorably change, and the results of all that dedicated beavering will be gone. And everything in and around it—the tanagers, the woodpeckers, the mayflies, the pines—will be affected, one way or another.

Some years back, before he took on organized religion, Richard Dawkins wrote a book called The Extended Phenotype. A phenotype is the physical manifestation of a genotype—the ensemble of physical traits that the genome codes for. Dawkins’ point was that you have to think of behavior as part of that ensemble, which is fair enough with beavers. Their dam-building drive is so hard-wired that if you play the sound of running water for captives, they’ll pile up sticks and brush in front of the speaker.

Beyond that, Dawkins’ notion of the phenotype also includes the built environment that results from an organism’s behavior—the dam, the pond, the lodge.

We tend to think of our species as the only one that leaves a significant mark on the world, for better or worse. Far from it: beyond the engineering of beavers, consider the cities of the termites or the coral polyps, the soil moved by pocket gophers. All of us, man to microorganism, shape our various environments.

And our environments shape us back. Another book from the ’80s, Richard Levins and Richard Lewontin’s The Dialectical Biologist, tried to make that point, albeit with too much Marxist jargon for most tastes. (With us, there’s another layer when culture feeds back into the genome, as when Northern European and East African cattle herders independently—by separate genetic pathways—evolved adult lactose tolerance.)

Woodpeckers—to pick just one of the cast of characters at Hat Lake—are builders and shapers in their own right. Their nesting cavities provide housing for a whole community of hole-nesting birds: chickadees, nuthatches, flycatchers, swallows, wrens. A woodpecker neighborhood tends to have high avian diversity. Small mammals like flying squirrels also adopt old woodpecker nests.

But it doesn’t stop there. Working in Lassen National Forest, not far from where we were, Kerry Farris and Steve Zack of the Wildlife Conservation Society and Martin Huss of Arkansas State University made an interesting discovery about woodpeckers. They mist-netted white-headed, hairy, and black-backed woodpeckers, swabbed their beaks, and cultured the contents of the swab in a petri dish. Half a dozen species of filamentous fungi, some known wood-decayers, were identified in the culture.

The woodpeckers seem to be carrying around little fungus colonies, inoculating the ponderosa pine snags where they feed with organisms that hasten the decay of the dead wood, making the birds’ foraging routines a little easier. Other cavity nesters like red-breasted nuthatches and mountain chickadees had their own fungus cultures; a control group of non-cavity-nesters—warblers, kinglets, tanagers, finches—did not.

The jury is still out on whether what’s going on with the woodpeckers and the fungi is dedicated mutualism or opportunistic hitchhiking, and who is part of whose extended phenotype. The more you look at the interface of ecology and evolution, the more complicated it seems to get.

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Update (July 19)
The study by Kerry Farris, Martin Huss and Steve Zack entitled "The Role of Foraging Woodpeckers in the Decomposition of Ponderosa Pine Snags" can be found here. The entire article requires access from a library or someone with BioOne Journal online access.

Encyclopedia of Life

Encyclopedia of Life (Press Release)
May 9, 2007 -- EOL

"We intend to make key components of the Encyclopedia available to the general public starting some time in 2008. As a ballpark estimate, we believe that we can produce the full encyclopedia in about 10 years."

A Leap for All Life: World’s Leading Scientists Announce Creation of “Encyclopedia of Life”
Biodiversity, Science Communities Unite Behind Epic Effort To Promote Biodiversity, Document All 1.8 Million Named Species on Planet

Many of the world’s leading scientific institutions today announced the launch of the Encyclopedia of Life, an unprecedented global effort to document all 1.8 million named species of animals, plants, and other forms of life on Earth. For the first time in the history of the planet, scientists, students, and citizens will have multi-media access to all known living species, even those that have just been discovered.

The Field Museum of Natural History, Harvard University, Marine Biological Laboratory, Smithsonian Institution, and Biodiversity Heritage Library joined together to initiate the project, bringing together species and software experts from across the world. The Missouri Botanical Garden has become a full partner, and discussions are taking place this week with leaders of the new Atlas of Living Australia. The Encyclopedia today also announced the initial membership of its Institutional Council, which spans the globe, and whose members will play key roles in realizing this immense project. An international advisory board of distinguished individuals will also help guide the Encyclopedia.

The effort is spurred by a $10 million grant from the John D. and Catherine T. MacArthur Foundation and $2.5 million from the Alfred P. Sloan Foundation, and will ultimately serve as a global beacon for biodiversity and conservation.

“The Encyclopedia of Life will provide valuable biodiversity and conservation information to anyone, anywhere, at any time,” said Dr. James Edwards, currently Executive Secretary of the Global Biodiversity Information Facility who today was officially named Executive Director of the Encyclopedia of Life. “Through collaboration, we all can increase our appreciation of the immense variety of life, the challenges to it, and ways to conserve biodiversity. The Encyclopedia of Life will ultimately make high-quality, well-organized information available on an unprecedented level. Even five years ago, we could not create such a resource, but advances in technology for searching, annotating, and visualizing information now permit us, indeed mandate us to build the Encyclopedia of Life.”

Over the next 10 years, the Encyclopedia of Life will create Internet pages for all 1.8 million species currently named. It will expedite the classification of the millions of species yet to be discovered and catalogued as well. The pages, housed at http://www.eol.org, will provide written information and, when available, photographs, video, sound, location maps, and other multimedia information on each species. Built on the scientific integrity of thousands of experts around the globe, the Encyclopedia will be a moderated wiki-style environment, freely available to all users everywhere.

“The Encyclopedia of Life will be a vital tool for scientists, researchers, and educators across the globe, providing easy access to the latest and best information on all known species,” said Jonathan F. Fanton, President of the John D. and Catherine T. MacArthur Foundation. “Technology is allowing science to grasp the immense complexity of life on this planet. Sharing what we know, we can protect Earth's biodiversity and better conserve our natural heritage.”

“For more than 250 years, scientists have catalogued life, and our traditional catalogues have become unwieldy,” said Ralph E. Gomory, President of the Alfred P. Sloan Foundation. “The Encyclopedia of Life will provide the citizens of the world a ‘macroscope’ of almost unimaginable power to find and create understanding of biodiversity across the globe. It will enable us to map and discover things so numerous or vast they overwhelm our normal vision.”

Scientists began creating individual web pages for species in the 1990s. However, Internet technology needed to mature to allow fast and efficient creation of a comprehensive Encyclopedia. While specific Encyclopedia of Life efforts, including the scanning of key research publications and data, have been underway since January 2006, work has accelerated due to the support provided by the John D. and Catherine T. MacArthur Foundation and the recent discussion of the Encyclopedia of Life by renowned biologist Edward O. Wilson at the March 2007 Technology, Entertainment, Design (TED) Conference.

One of the world’s foremost scientists and environmentalists, Wilson, professor emeritus at Harvard University, “wished” for the establishment of the Encyclopedia of Life during his TED Conference address. Noting that “our knowledge of biodiversity is so incomplete that we are at risk of losing a great deal of it before it is ever discovered,” Wilson called for a contemporary, dynamic portrait of the living Earth.

“I wish that we will work together to help create the key tool that we need to inspire preservation of Earth’s biodiversity: the Encyclopedia of Life,” Wilson said at TED. “What excites me is that since I first put forward this idea, science has advanced, technology has moved forward. Today, the practicalities of making this encyclopedia real are within reach as never before.”

Ultimately, the Encyclopedia of Life will provide users the opportunity to personalize the learning experience through its “my eol” feature. The site can be made available in all major languages and will connect scientific communities concerned with ants to apples to zebras. As part of its work, the Encyclopedia of Life will collaborate and partner with a wide range of organizations, individuals, and experts to help strengthen the Encyclopedia and its impact on communities throughout the world.

“The solidarity of the U.S. and global communities for the Encyclopedia of Life is tremendously exciting and lifts my confidence that this vast, romantic global effort will succeed,” Edwards said. “We are also encouraged by the declaration in March 2007 by the environment ministers of the G8 nations to foster a global species information system.”

While initial work will emphasize species of animals, plants, and fungi, the design can be extended to encompass microbial life.

To provide depth behind the portal page for each species, the Biodiversity Heritage Library (BHL), a consortium that holds most of the relevant scientific literature, will scan and digitize tens of millions of pages of the scientific literature that will offer open access to detailed knowledge. In fact, the BHL now has scanning centers operating in London, Boston, and Washington DC, and has scanned the first 1.25 million pages for the Encyclopedia.

“I dream that in a few years wherever a reference to a species occurs on the Internet, there will be a hyperlink to its page in the Encyclopedia of Life,” concluded Edwards.


ABOUT THE ENCYCLOPEDIA OF LIFE
The Encyclopedia of Life is a collaborative scientific effort led by the Field Museum of Natural History, Harvard University, Marine Biological Laboratory, Missouri Botanical Garden, Smithsonian Institution, and Biodiversity Heritage Library, a consortium including the core institutions and also the American Museum of Natural History (New York), Natural History Museum (London), New York Botanical Garden, and Royal Botanic Gardens (Kew). Ultimately, the Encyclopedia of Life will provide an online database for all 1.8 million species now known to live on Earth. When completed, http://www.eol.org will serve as a global biodiversity tool, providing scientists, policymakers, students, and citizens information they need to discover and protect the planet and encourage learning and conservation.

Voluntary Restrictions Protect Quarter of World's High Seas from Trawling

Nations seek end to trawling seas
May 5, 2007 -- Associated Press via CNN

More than 20 nations agreed Friday to discourage unregulated and destructive bottom trawling on the South Pacific high seas, a victory for environmental groups.

The agreement, which takes effect September 30, is intended to protect about a quarter of the world's high seas, a vast area extending roughly from the Equator to the Antarctic Circle and from Australia and New Zealand to the west coast of South America.

Observers and ship locator monitoring systems are to be used, and vessels must remain at least five nautical miles (9,260 meters) from deep-water corals and other vulnerable marine ecosystems.

The agreement reached in Renaca, Chile, follows a U.N. General Assembly resolution in December aimed at getting tough on high-seas bottom trawling, which involves fishing boats that drag giant nets along the sea floor.

Enormously effective at catching fish, the nets also wipe out almost everything in their path, smash coral and stir clouds of sediment that smother sea life, marine experts say.

Orange roughy is the main commercial fish in the South Pacific high seas, mainly caught by New Zealand fishing vessels. Estimates of the fishing trade range up to about $10 million (euro7.4 million).

New Zealand officials agreed to the voluntary restrictions in the South Pacific high seas, but they said the restrictions could "severely constrain" its fishing vessels. The ecological costs of the huge nets are far higher, environmental groups said.

"This area contains thousands of these underwater sea mountains, or seamounts, that are considered to be some of the most ecologically rich habitats in the world," said Joshua Reichert, director of the private Pew Charitable Trusts' environment division, which coordinated the groups' campaign. "For all of us, this really represents a major step forward for marine conservation."

A U.N. report last year called bottom trawling a danger to unique and unexplored ecological systems. It said slightly more than half the underwater mountain and coral ecosystems in the world can be found beyond the protection of national boundaries.

The new agreement is among members of the fledgling South Pacific Regional Fisheries Management Organization: Australia, Canada, Chile, China, Colombia, Cook Islands, Ecuador, the European Commission, Federated States of Micronesia, France, Japan, New Zealand, Niue, Palau, Papua New Guinea, Peru, Russia, South Korea, Ukraine, the United States and Vanuatu.

Biological Look At Marmosets And Chimerism

Funky monkeys (Subscription)
March 29, 2007 -- The Economist

Marmosets give birth to their genetic nieces and nephews.

It does not take a biologist to tell that there are two sorts of twins. Twins can be genetically identical or they can be as different as siblings that were born at different times. Most marmosets, though, fall somewhere in between. These small New World monkeys may be cute, but they are chimeras nonetheless. Like the monster from Greek mythology, many marmosets are a mixture of more than one individual. They are, genetically, both themselves and their sibling at the same time.

There are two other odd (and indeed cute) things about marmosets. One is that they are always conceived as twins. The other is that they are unusually caring towards one another. Fathers are particularly and peculiarly doting. Now Corinna Ross and her colleagues at the University of Nebraska have found evidence to suggest the former oddity explains the latter. They have done so by showing that chimerism extends to all sorts of tissues, including marmoset sex cells.

That insight arose when Dr Ross DNA-fingerprinted 12 types of tissue from 39 dead marmosets, in order to work out how frequently cells containing a twin's genome occurred in different parts of the body. Marmosets are not equal mixtures of two genetic individuals. They become chimeras not because their embryos merge but because more often than not their placentas do. They thus share their embryonic blood supplies. That allows them to exchange stem cells, which then develop into more specialised sorts of cell in their new bodies.

Chimeric cells were scattered everywhere, including the sex cells. This means that, in principle, a marmoset can either father (if male) or give birth to (if female) a baby that is its niece or nephew rather than its son or daughter.

To find out if this actually happens, Dr Ross turned her attention to living marmosets. She used hair, blood and saliva samples to identify chimeric animals among the 36 sets of twins in her colony. First, as she reports in this week's Proceedings of the National Academy of Sciences, she proved the marmosets made babies from their chimeric sex cells. This happened even when the twins were brother and sister rather than being of the same sex.

That is bizarre, because female mammals have two copies of the X chromosome, and males have one X and one Y. Any chimeric female that passed on her twin brother's genes must have developed eggs from an XY stem cell instead of the normal XX. Conversely, a chimeric male that passed on his twin sister's genes grew sperm from an XX stem cell, rather than XY. Dr Ross found examples of both.

This done, she tried to work out whether chimerism influenced parental care in marmosets. Zoologists think of caring for others as selfish behaviour, which animals only bother with to improve the chances of their genes being passed on to future generations. Creatures therefore help to bring up babies only to the extent that they believe they are related to them. In marmosets, caring means carrying, so Dr Ross recorded the time each baby marmoset was carried by its mother and by its father during the first fortnight of life. Mothers spent less time carrying those of their offspring who were chimeras than they did carrying those that were non-chimeric. Fathers, however, behaved in the opposite way.

Why that happened is not clear. But one possibility is that, in a species in which females routinely mate with several males, chimerism evolved as a way of duping males into looking after offspring that are not their own. Chimerism, in other words, might confuse a male who fathered one twin into thinking he is dad to both.

This could happen because a chimeric twin that grew from an egg which his sperm did not fertilise would nonetheless have some skin cells containing his genes. The scent-producing cells of that skin would give off pheromones signalling his paternity. Thus by mixing two fathers' genes between two infants, a female creates a situation in which both males consider it in their interest to care for both offspring—a double bonus.

US biofuels: A field in ferment

US biofuels: A field in ferment (Subscription)
December 7, 2006 -- By Katharine Sanderson, Nature

To move US biofuels beyond subsidized corn will be a challenge, reports Katharine Sanderson.

Critics of the US ethanol industry have long derided it as an environmentally questionable subsidy to Mid-western farmers that simply serves a transparently political purpose. Voters in Iowa, the buckle in the US corn belt, get first say in the process of choosing presidential candidates. All such candidates are in favour of turning corn (maize), which the state produces in abundance, into ethanol. This pre-presidential support is good for the Iowan economy, but not necessarily that great for the environment.

Studies that compare the energy that goes into making ethanol — expended during the harvesting, fertilizing and transporting of the corn to refineries, and then refining it — with the energy that is released when it is burned routinely show that the net gain is at best small. The American Coalition for Ethanol says that ethanol contains twice the amount of energy that is used to make it; critics see no net gain whatsoever.

This criticism has had little effect, and since 1980, US ethanol production has risen from an average of 6,500 barrels (1 million litres) a day to 260,000 barrels a day. Federal mandates call for a further doubling by 2012. But it is increasingly clear to many in the industry that the criticisms of corn-based ethanol have merit, and in 2006, the need for an alternative was given the highest profile it could get when President George W. Bush brought it up in his state of the union address. In order to improve US energy security, he said, his government intended to make cellulosic ethanol (ethanol made from the rougher and woodier parts of plants) a competitive biofuel within six years.

Corn stores
The advantage of an ear of corn as a source of ethanol (or for that matter as a bit of food) is that it is mainly starch, which is made up of sugars linked in a regular way with bonds that can be broken easily. Breaking the bonds between sugars and using yeast in the fermentation to produce ethanol is a straightforward task for the biorefineries. The disadvantage is that corn is a crop that needs a lot of inputs — fertilizers, water and pesticides — and that doesn't put as much of the sugar it creates through photosynthesis into its ears as one might wish. A lot of the sugar is instead turned into stalks and 'stover' — structural material rich in cellulose and considerably more difficult to break down.

Plants that store up a significant amount of energy in easily usable forms such as starch or sugar are exceptions, encouraged in their oddities by millennia of selective breeding — and of them all, only sugar cane grown in the tropics puts enough energy into its easily purified products to make bioethanol obviously attractive. Most plants put the bulk of the energy they store up from the sun into cellulose and a related polymer, hemicellulose, and woody plants add another substance, lignin, to the mix. Cellulose makes up the plant's cell walls and, like starch, it is a polymer of sugars containing six carbon atoms linked one to the next. Hemicellulose, on the other hand, is based on a five-carbon sugar, xylose, although it contains many other sugars as well; its various components are thrown together in messy looking chains with many branches. Lignins are huge crosslinked jumbles of organic molecules which reinforce cellulose and hemicellulose to turn them into wood.

The energy that the plants put in to making the bonds in these various substances could, in principle, be extracted by fuel makers. And these molecules — particularly cellulose, which is both the most abundant and the easiest to dismantle — are much more plentiful than starches and sugars. But they are also much harder for microbes to break down; if they weren't, there'd be no trees, just pools of green goo. As yet, there are no cellulosic ethanol refineries operating at full commercial capacity, and assessments of the technology's readiness for market vary a great deal, as do opinions on how to get there from here. Government incentives and tax breaks might be one solution, but big energy companies also have a role to play, as do the smaller companies that have already worked on developing the technology, but have not yet found the best ways of spreading and licensing it.

The most expensive part of making ethanol from cellulose is pretreating the biomass to make it accessible to the enzymes that will then cut the sugars from the polymers so that they can be fermented. Typical pretreatments reduce the feedstock's volume chemically using acids, peroxides and ammonia, often along with some form of mechanical pressing or shredding. Unfortunately, this is not a step that can be skipped to cut costs, says Charles Wyman of the University of California, Riverside, because high sugar yields are essential, and untreated biomass gives very low yields. "The only step more expensive than pretreatment is no pretreatment," he says. Instead, the hunt is on for pre-treatment technologies that involve fewer chemicals, require less energy and don't degrade the sugars that are set free in the process.

After the pre-treatment stage comes the snipping out of the sugars, which is the point at which biotechnologists think they can greatly improve on the current process. Abengoa Bioenergy of St Louis, Missouri, a subsidiary of the Spanish engineering group Abengoa, recently invested $10 million in Dyadic International, a biotechnology company that is concentrating on enzymes for degrading cellulose.

Based in Jupiter, Florida, Dyadic didn't start out as an energy company — in the 1970s it was a leading supplier of pumice for stonewashing jeans. But the enzymatic expertise it developed for distressing denim was then turned to a number of other ends. One of those was breaking down wood, a job that in nature largely falls to fungi. The company's research has centred on a filamentous mess of a fungus discovered by accident in a Russian forest that now, after ten years of processing and genetic engineering, makes up Dyadic's patented C1 fungal cell system. The fungus has been fully sequenced and encouraged to overexpress the genes that then make cellulases and xylanases — the proteins that break up cellulose and hemicellulose to produce fermentable sugars. "We have the world's most prolific filamentous fungus," boasts Dyadic's chief executive Mark Emalfarb.

Cellulose solutions
Emalfarb believes that the cellulosic ethanol market could eventually be worth $20 billion a year in the United States, and suggests that there is enough raw material available in the United States to produce 2.4 billion barrels of cellulosic ethanol a year. This is a bit more than half of what some estimates claim is needed to completely replace petrol as a fuel — the United States gets through some 3.3 billion barrels a year, but the energy content of ethanol is lower than that of petroleum.

The current leader in the cellulosic ethanol market, Iogen, also uses fungal enzymes. The company makes small commercial quantities of ethanol from straw at its pioneering cellulosic ethanol facility in Ottawa, Canada. As the first of its kind, this is an undoubted achievement. But even when it reaches its full capacity, which it is taking quite some time to do, it will be capable of producing only 2.5 million litres (16,000 barrels) a year, which is not a great deal.

Iogen chief executive Brian Foody is not worried. The critical steps for getting the right enzymes, the right pretreatment systems and the right yeast systems, have all been done, he says. "We just need to go through the nuts and bolts of the process." This means making sure that the demonstration plant works well enough to be replicated elsewhere — the company is looking to build new facilities in Idaho, Saskatchewan and Germany.

Iogen recently secured a $30-million investment from the bankers Goldman Sachs, bringing the total invested in it since the 1970s up to $130 million. But not all potential investors are convinced. "I don't really understand what Iogen is doing," says Matt Drinkwater, market analyst at New Energy Finance in London, UK. And his concerns are not unique to Iogen — many of the companies in the sector, he says, hold details of their processes so close to their chests that they are hard to evaluate, whether they be relatively small outfits such as Iogen or giants such as DuPont, which is also developing cellulosic ethanol technologies. Robert Wilder, who manages the Wilderhill clean energy index — the first such index to be accepted on Wall Street — agrees, but acknowledges the constraints that the chief executives of small cellulosic ethanol companies work under in terms of not tipping their hands to larger competitors.

Smells like green spirit
Perhaps because of these uncertainties over the technology's readiness, most of the money that has been invested recently in ethanol production both within the United States and beyond has been in the more traditional technologies. The sizable investments being made by agribusiness giant Archer Daniels Midland — the biggest ethanol producer in the United States and, perhaps tellingly, a company run by a chief executive who was recruited from the oil industry — seem mostly to be in traditional corn ethanol. The same applies to high-flying UK entrepreneur Richard Branson's recent investments in Ethanol Grain Processors of Tennessee and a new grain-based Californian ethanol venture, Cilion.

But there is some evidence that enthusiasm for investing in corn ethanol may be waning. Various ethanol companies that were riding high earlier in the year saw their stock slump after the summer when oil prices came down from their $78 a barrel peak.

This might mean the market is aware that, although subsidies may be able to keep it profitable for the time being, there is no way that corn ethanol can make a marked difference to long-term energy use in the United States. To make enough ethanol to start seriously displacing oil imports requires a process that can use cellulosic materials such as switchgrass, a tall prairie grass, or miscanthus, a grass imported from Asia, which provide far more tonnes of biomass per hectare than corn kernels ever can, and can be grown on land not suitable for conventional agriculture. Other sources could be farm waste or trees or newly engineered plants of some sort.. This leads to something of an investing impasse: the companies in the business at the moment make money; the ones that might take it to the next stage do not, in large part because no one has made the heavy capital investments needed for plants that make use of the technologies that have already been piloted.

One way round this is to invest across the board. This is the strategy pursued by Vinod Khosla, the Silicon Valley venture capitalist who is one of the founders of Cilion. Khosla is also involved in cellulosic technologies through two companies based in Cambridge, Massachusetts: Celunol, which has just started to operate its own pilot plant, and Mascoma, which concentrates on process engineering and which last month raised $30 million in second-round venture funding. Farther afield in the biofuels world, Khosla is also a major investor in Kergy, a company that turns biomass into fuel in a completely different 'thermochemical' way, using just heat and catalysts. For some observers, such as Dan Schrag, a geochemist at Harvard University, these approaches are more attractive than fermentation, not least because they need no witches' brews made from fiddly feedstock-specific enzyme. "When the dust clears, cellulosic ethanol is unlikely to be where we end up," he predicts.

To Drinkwater, investors such as Khosla, with their broad-based approach to the problem, are exactly what the industry needs to drive the market forwards and get it over the final bump it needs to clear before commercial success. Unfortunately, there are few such people. In their absence, many in the industry, not without self-interest, see the responsibility resting with governments to provide attractive tax incentives. "All forms of energy should face market prices that reflect the cost to society that they impose," says Foody. And to set those market prices, the right tax incentives and government mandates need to be in place.

But government incentives won't make the scientists any smarter, and observers outside the pioneering companies believe there is still basic work to be done before those companies, or their eventual competitors, make the process economically viable. Thus they welcome increasing levels of basic research from the government, such as the US Department of Energy's pledge of $250 million to set up two bioenergy research centres that are largely focused on cellulosic ethanol. The European Union has set aside E100 million (US$132 million) for cellulosic ethanol in its seventh Framework Programme on research.

Ethanol alternative
Companies large enough to afford it are also following the basic research route rather than placing early bets on particular technologies. BP has announced it will invest $500 million over ten years to fund an Energy Biosciences Institute, which will be a dedicated facility based at a university. The University of Cambridge, Imperial College London, Massachusetts Institute of Technology, Stanford, the University of California, Berkeley, and Lawrence Berkeley National Laboratory have all been mentioned as possible hosts — the final decision is expected in December.

One intriguing possibility for such research to pursue is replacing ethanol with another form of alcohol. The fact that ethanol is easy to ferment can blind people to the fact that it has almost as many inherent problems as a fuel as corn has as a feedstock. Its tendency to pick up water wherever it goes makes it hard to transport, particularly in pipelines. It's corrosive. It's more volatile than one might wish. And its energy density is low compared with regular petrol.

For these reasons, BP and DuPont are working with British Sugar to adapt their ethanol fermentation facility in East Anglia to produce butanol — an alcohol with four carbons in it, as opposed to ethanol's two. This requires training microbes in new tricks, but it is not as hard a problem as breaking down woody plant material. The East Anglia plant will use locally grown sugar beet as the feedstock, but in the long term the aim would be to use a cellulosic feedstock. "We accept that taking stuff out of the food chain is not the right way to go," says Robert Wine, a BP spokesman.

Drinkwater thinks that an industry demand for butanol as an end product could actually increase interest in cellulosic approaches. "Most refiners would be much happier to use butanol than ethanol," he says. If oil companies become confident in biofuel technologies, investors would in turn be more confident of the biofuels industry as a whole, giving the industry that elusive final shove that it seems to need.

Frilled Shark (Chlamydoselachus anguineus)

This video shows rare footage of a frilled shark in shallow water after it was captured.

Seeds of Hope

In this weeks edition of The Economist, an article enititled 'Seeds of hope' discusses "An international seed bank being set up in the Arctic". Here is the article:

If catastrophe were to befall humanity—be it plague, nuclear war or an asteroid striking the Earth—what provision could be made for the survivors? This week work began on a project to re-establish agriculture should such a calamity occur. On a remote Arctic island, a vault is being dug to house the seeds of up to 3m different crops, as part of plans to protect food supplies across the world.

The Svalbard International Seed Vault, as the facility is called, will cost the Norwegian government, which is paying for it, about $3m. Eventually it will contain samples of every known crop variety that can be grown from seed, from the tropics to the highest latitudes.

Svalbard was chosen because it is cold and remote. The island is expected to remain frozen for the next hundred years, despite changes in the world's climate, and the vault is being carved out of the ice and rock. Seeds deposited in the bank will be preserved by the cold, certainly for hundreds and perhaps even thousands of years. The freezing conditions, not to mention polar bears, should put off any unwelcome visitors. Just in case they do not, the bank will be 70 metres (230 feet) underground, inside concrete walls more than a metre thick and behind a strong security door and a perimeter fence.

The Global Crop Diversity Trust, a charity involved in the creation of the vault, estimates that there are now some 1,400 gene banks for crops, scattered on every inhabited continent. It is developing plans to conserve every important crop on the planet. Some do not have seeds and so cannot be stored on Svalbard. Bananas, for example, are estimated by the United Nations Food and Agriculture Organisation to be the world's fourth most consumed food (after wheat, rice and maize) and form the staple diets of some 400m people in the tropics. Bananas can only be conserved as cuttings, and these must be cut back and replanted every few months. Work is under way to develop better ways of preserving such crops.

Many of the gene banks are in countries where the crop is not native, to make it more likely that the species will survive a disaster. (The banana bank is in Belgium.) The Svalbard vault fulfils this criterion for any seed you can think of. Whether anyone will be able to reach it if catastrophe strikes is another question.

R.I.P. Harriet the Tortoise

On June 23rd 2006 "Harriet the tortoise, one of the world's oldest known living creatures, died in Australia aged about 175." Here is the article from BBC News:

Senior vet Dr John Hangar told Australia's ABC that Harriet, a Giant Galapagos tortoise, had died of heart failure after a short illness. "She had a very fairly acute heart attack and thankfully passed away quietly overnight," Dr Hangar said.

Last year staff at Australia Zoo, where Harriet had lived for 17 years, held a party to celebrate her 175th birthday. Some people believe that Harriet was studied by British naturalist Charles Darwin. Darwin took several young Giant Galapagos tortoises back to London after his epic voyage on board HMS Beagle.

DNA testing has suggested the giant creature was born around 1830, a few years before Darwin visited the Galapagos archipelago in 1835. However, Harriet belonged to a sub-species of tortoise only found on an island that Darwin never visited.

At the time of her 175th birthday party, Harriet weighed 150kg (23 stone) and was roughly the size of a dinner table. She was the star attraction at the Australia Zoo on Queensland's Sunshine Coast. Her keepers put her longevity down to a stress-free life.

Giant Panda Scat Survey

On June 20th 2006, Helen Briggs wrote this encouraging article for the BBC on a recent survey of Giant Pandas.

Fears that the giant panda is on the brink of extinction may be unjustified, research suggests.

Scientists believe populations have been underestimated in past surveys and there may be as many as 3,000 pandas left in the wild. Numbers in reserves could be restored if conservation efforts continue, they write in Current Biology. The panda once inhabited much of China but is now found only in the forested mountain areas of the country. Its survival has become a cause celebre of the conservation movement, attracting worldwide attention. The giant panda has long suffered at the hands of poachers and loggers, and was hit by the large-scale die-off of bamboo in the 1980s. Numbers in the wild have been put at about 1,000 but the animal's elusive and wary nature has made it difficult to conduct accurate censuses.

Previous surveys have used conventional techniques which estimate how many pandas there are based on the amount of droppings found in a given area. However, researchers in China and the UK tried out a new hi-tech method based on analysing DNA recovered from panda droppings. This enables individuals to be identified and tracked across a wide area, giving information on their age and sex.

The study also provides evidence that pandas in the most important habitat of its kind have not suffered genetically over this period - there is no evidence of the sort of inbreeding or low genetic diversity that might threaten the species' long-term survival. "DNA profiling in pandas can give us much more precision in identifying individuals and hence population numbers," said study co-author Prof Michael Bruford of Cardiff University, UK.

The results suggest that about 66 pandas live in the Wanglang Nature Reserve in Sichuan Province, more than twice as many as were estimated in a survey conducted in 1998. "If that were to be repeated across the range there could be as many as 2-3,000 pandas in the wild but a very important point is that this work needs to be replicated in other reserves," he added.

Conservationist groups stress that moves to protect the panda through bans on poaching and deforestation must be maintained. Half of the panda's mountainous bamboo habitat was lost between 1974 and 1988. There are now 40 panda reserves in China compared to 13 two decades ago. "Whilst this is potentially exciting and promising news, it also reinforces the fact that giant panda numbers are still dangerously low," said Mark Wright, Conservation Science Advisor at WWF-UK. "It looks like we are moving in the right direction but we must continue with our efforts to conserve this species and the threats to its habitat if it is going to survive in the long-term."

Mountain Gorilla Munchies

In the May 5th 2006 issue of Science/AAAS, this random sample edited by Yudhijit Bhattacharjee explains why Mountain Gorillas, and possibly other primates, crave rotting wood.

Mountain gorillas love to munch on rotting wood, and now we know why: The food is a source of sodium. Researchers from Cornell University reported in a study published online in Biology Letters on 25 April that gorillas in Uganda get more than 95% of their sodium requirements from decaying wood, which makes up only 4% of their diet. They also found that the apes avoided timber with low sodium content. The researchers plan to see if this taste for salty wood is common in other primate species.

Medicine Needs Evolution

Dr. Jerry Downhower of The Ohio State University Department of E.E.O. Biology and author of many distinguished books recently posted the Science article entitled 'Medicine Needs Evolution' on his office door.

On February 24th, 2006 Science/AAAS published this article describing multiple reasons why evolution deserves to be recognized as a basic science for medicine.

The citation of 'Evolution in Action' as Science's 2005 Breakthrough of the Year confirms that evolution is the vibrant foundation for all biology. Its contributions to understanding infectious disease and genetics are widely recognized, but its full potential for use in medicine has yet to be realized. Some insights have immediate clinical applications, but most are fundamental, as is the case in other basic sciences. Simply put, training in evolutionary thinking can help both biomedical researchers and clinicians ask useful questions that they might not otherwise pose.

Although anatomy, physiology, biochemistry, and embryology are recognized as basic sciences for medicine, evolutionary biology is not. Future clinicians are generally not taught evolutionary explanations for why our bodies are vulnerable to certain kinds of failure. The narrowness of the birth canal, the existence of wisdom teeth, and the persistence of genes that cause bipolar disease and senescence all have their origins in our evolutionary history. In a whole array of clinical and basic science challenges, evolutionary biology is turning out to be crucial. For example, the evolution of antibiotic resistance is widely recognized, but few appreciate how competition among bacteria has shaped chemical weapons and resistance
factors in an arms race that has been going on for hundreds of millions of years. The incorrect idea that selection reliably shapes a happy coexistence of hosts and pathogens persists, despite evidence for the evolution of increased virulence when disease transmission occurs through vectors such as insects, needles, or clinicians’ hands. There is growing recognition that cough, fever, and diarrhea are useful responses shaped by natural selection, but knowing when is it safe to block them will require studies grounded in an understanding of how selection shaped the systems that regulate such defenses and the compromises that had to be struck.

Evolution is also the origin of apparent anatomical anomalies such as the vulnerabilities of the lower back. Biochemistry courses cover bilirubin metabolism, but an evolutionary explanation for why bilirubin is synthesized at all is new: It is an efficient free-radical scavenger. Pharmacology emphasizes individual variation in genes encoding cytochrome P450s, but their evolutionary origins in processing dietary toxins are just being fully appreciated. In physiology, fetal nutritional stress appears to flip an evolved switch that sets the body into a state that protects against starvation. When these individuals encounter modern diets, they respond with the deadly metabolic syndrome of obesity, hypertension, and diabetes.

The triumphs of molecular biology call attention to evolutionary factors responsible for certain genetic diseases. The textbook example is sickle-cell disease, whose carriers are resistant to malaria. Similar protection against infection has been hypothesized for other disorders. Which aspects of the modern environment are pathogenic? We need to find out. Increases in breast cancer have been attributed to hormone exposure in modern women who have four times as many menstrual cycles as women in cultures without birth control. Other studies suggest that nighttime exposure to light increases the risk of breast cancer by inhibiting the normal nighttime surge of melatonin, which may decrease tumor growth. Evolution has also provided some explanations for conditions such as infertility. The process that eliminates 99.99% of oocytes may have evolved to protect against common genetic defects. And some recurrent spontaneous miscarriages may arise from a system evolved to protect against investing in offspring with combinations of specific genes that predispose to early death from infection.

These and other examples make a strong case for recognizing evolution as a basic science for medicine. What actions would bring the full power of evolutionary biology to bear on human disease? We suggest three. First, include questions about evolution in medical licensing examinations; this will motivate curriculum committees to incorporate relevant basic science education. Second, ensure evolutionary expertise in agencies that fund biomedical research. Third, incorporate evolution into every relevant high school, undergraduate, and graduate course. These three changes will help clinicians and biomedical researchers understand that both the human body and its pathogens are not perfectly designed machines but evolving biological systems shaped by selection under the constraints of tradeoffs that produce specific compromises and vulnerabilities. Powerful insights from evolutionary biology generate new questions whose answers will help improve human health.

Don't Pray for Me!

MSNBC posted this article by the Associated Press on March 30th 2006. The abstract can be found here at the American Heart Journal.

In the largest study of its kind, researchers found that having people pray for heart bypass surgery patients had no effect on their recovery. In fact, patients who knew they were being prayed for had a slightly higher rate of complications.

The study looked at complication rates within 30 days of heart bypass surgery and compared three groups of about 600 each: those who knew they were being prayed for, those who were prayed for but only knew it was a possibility, and those who weren’t prayed for but were told it was a possibility.

Results showed no effect of prayer on complication-free recovery. But 59 percent of the patients who knew they were being prayed for developed a complication, versus 52 percent of those who were told it was just a possibility.