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The Right Way to Warm Up Is (Your Answer Here)
By GINA KOLATA, The New York Times, May 17, 2010
At the Boston Marathon last month, my running partner, Jen Davis, said things were pretty much the same as the 10 other times she has run this race. Most runners stood around waiting for the race to start. Some did strides — short bursts of speed — or ran briefly at close to their race pace. There was a lot of stretching, too, and applications of heat rubs like Bengay and jumping up and down to stay warm.
My son, Stefan Kolata, was with the elite men this year in Boston and warmed up with them in their own special pre-race area. Those runners had a very different routine, he says. They spent about 15 minutes doing sort of a slow shuffle. There they were, a long line of elites, going around and around the warm-up area, barely lifting their legs.
Then, some went to a parking lot and did dynamic stretching — high knees, backward running, sideways running. Others vanished from the outdoor warm-up area, emerging again when the race was about to begin.
When it was all over, the men’s winner finished in 2:05:52, an average pace of 4 minutes 48 seconds per mile. Even the 10th-place finisher had a time of 2:10:33, or 4:59 a mile. So maybe these fast men know a secret about warm-ups.
Or maybe not.
Just about every serious competitive athlete, it seems, warms up before a race or even a training session. But there seems to be no particular method to their warm-ups.
Some, like Paula Radcliffe, the world record holder for the women’s marathon, spend more time warming up than most people spend running.
“Warm-up usually takes 45 to 50 minutes and is pretty much the same for workouts and races,” she told me. It consists of jogging for 10 to 20 minutes, stretching, and then doing strides.
But her warm-up is short and easy compared with the cyclist Andy Hampsten’s 90-minute warm-up before a time trial, in which cyclists ride one by one as fast as they can over a course that is typically about 25 miles.
Mr. Hampsten, who rode in the Tour de France and was the only American ever to win the Tour of Italy, began his warm-up with 30 minutes of easy riding followed by 40 minutes in which he rode as hard as he could for intervals of 2 minutes, alternating with 5 minutes at an easy pace, followed by 20 more minutes of easy riding. He said he knew he was warmed up when he got “a mild endorphin buzz.”
At the other extreme is the Olympic swimmer Dara Torres.
“I don’t need a ton of warm-up to be ready for my races,” she said. Her warm-up is just “some light swimming, kicking and drills,” followed by a few sprints.
Exercise researchers say they are not surprised by the lack of consensus on warming up. There is a theory of why it should improve performance, but there is dearth of good research on whether it actually does.
The theory, said Paul Laursen, a performance physiologist at the Millennium Institute of Sport and Health, in Auckland, New Zealand, is that muscles contract better after they have already been contracting.
As a muscle warms up, the force of its contractions can be charted like a staircase: when it starts to work, the contractions may be only half as strong as they are after it has contracted a few times. The explanation is that the contractions release calcium ions in the cells, enabling the muscle fibers to contract more forcefully. At the same time, muscle enzymes, which work best when slightly higher than body temperature, heat up and become more efficient.
That may be why the elite male marathoners did well after their slow shuffles. “Despite the fact that they can go so fast,” Dr. Laursen said, it will take only a few muscle contractions for their muscles to warm up effectively for their long duration event.”
But the story may be different for shorter events. Dr. Laursen said that athletes might do best with a high-intensity warm-up, the sort that Andy Hampsten did; that can allow fast-twitch muscle fibers to contract more efficiently and can prepare the nerve fibers and the cardiovascular system for an all-out effort.
That, at least, is the theory. What’s missing is evidence showing actual effects on performance.
There’s almost nothing credible, as Andrea J. Fradkin an exercise researcher at Bloomsburg University of Pennsylvania, discovered when she searched for published studies on warm-ups. Most of the research was done in the 1960s and ’70s, she told me, and its quality was poor.
In a recent review article she wrote, “Many of the earlier studies were poorly controlled, contained few study participants and often omitted statistical analysis.”
The studies were of so little value, she concluded, that “it is not known whether warming up is of benefit, of potential harm, or having no effect on an individual’s performance.”
An exception is Dr. Fradkin’s own studies of warming up before playing golf. After a decade of research, she found that a seven-and-a-half-minute warm-up involving cardiovascular exercise, stretching and air swings — swinging a golf club without hitting a ball — can significantly improve performance.
But that does not necessarily mean the same routine will work in other sports. As Dr. Fradkin put it, “How can you compare improving performance in golf with improving performance in swimming?”
It’s an appalling situation, she told me. Serious athletes place so much emphasis on warming up, yet what they do is based more on trial and error than on science. For now, she said, what to do “is almost a ‘he said, she said’ thing.”
Creatures of Cambrian May Have Lived On
By JOHN NOBLE WILFORD, The New York Times, May 17, 2010
Ever since their discovery in 1909, the spectacular Burgess Shale outcrops in the Canadian Rockies have presented scientists with a cornucopia of evidence for the “explosion” of complex, multicellular life beginning some 550 million years ago.
The fossils, all new to science, were at first seen as little more than amazing curiosities from a time when life, except for bacteria and algae, was confined to the sea — and what is now Canada was just south of the Equator. In the last half century, however, paleontologists recognized that the Burgess Shale exemplified the radiation of diverse life forms unlike anything in earlier time. Here was evolution in action, organisms over time responding to changing fortunes through natural experimentation in new body forms and different ecological niches.
But the fossil record then goes dark: the Cambrian-period innovations in life appeared to have few clear descendants. Many scientists thought that the likely explanation for this mysterious disappearance was that a major extinction had wiped out much of the distinctive Cambrian life. It seemed that the complex organisms emerging in the Cambrian had come to an abrupt demise, disappearing with few traces in the later fossil record.
Not everyone was convinced, however, and now a trove of 480-million-year-old fossils in Morocco appears to strike a blow to the idea of a major extinction. The international team of scientists who discovered the 1,500 fossils said their find shows that the dark stretch in the fossil record more probably reflects an absence of preservation of fossils over the previous 25 million years.
The team reports in the current issue of the journal Nature that the large number of “exceptionally preserved” Moroccan species exhibits apparently strong links to Cambrian species known from fossil beds in China, Greenland and, most notably, the Burgess Shale. The scientists think this solves the mystery. The Moroccan fossils, they said, establish that Burgess Shale-type species “continued to have an important role in the diversity and ecological structure of deeper marine communities well after the Middle Cambrian.”
The Moroccan fossils include sponges, worms, trilobites and mollusks like clams, snails and relatives of the living nautilus. Another fossil was similar to today’s horseshoe crab, a biological throwback familiar to beachcombers. Now, the scientists said, its antiquity appears to be even greater — some 30 million years earlier than previously thought, possibly in the late Cambrian.
The discovery team’s principal scientist and lead author of the journal article was Peter Van Roy, a Belgian paleontologist who is a postdoctoral fellow at Yale University. He has worked in Moroccan fossil beds the last 10 years, but it was only last year on a field trip, financed by the National Geographic Society, that he and other scientists uncovered the riches of a site near the Atlas Mountains and the city of Zagora.
Scientists from Britain, France, Ireland, Morocco and the United States participated in the research and were co-authors of the team report. A local fossil collector, Mohammed Ou Said Ben Moulal, directed Dr. Van Roy to the rock outcrops he had scouted.
Soon it became clear, Dr. Van Roy said last week in an e-mail message from Morocco, that the team had “really discovered the whole gamut of these Burgess animals, the majority of which had never been found after the Middle Cambrian.”
A leading member of the team, Derek E. G. Briggs, director of the Peabody Museum of Natural History at Yale, cut his academic teeth studying the Burgess Shale. Dr. Briggs figured prominently in “Wonderful Life: The Burgess Shale and the Nature of History,” the 1989 book by Stephen Jay Gould about what the author called the “weird wonders” of the Cambrian period.
In the book, Dr. Gould, who died in 2002, pondered the mystery of the relatively sudden burst of new life designs in the Cambrian, followed by their apparent disappearance. “What turned it off so quickly?” he asked. A few pages before, quoting Charles Darwin, he seemed to despair of finding the fossils to answer the question.
“Darwin wrote,” Dr. Gould recalled, “that our imperfect fossil record is like a book preserving just a few pages, of these pages few lines, of the lines few words, and of those words few letters.”
Darwin’s metaphor pertained to the chances of preservation for bones and teeth. So referring to the predominance of soft-body anatomies of Cambrian life, Dr. Gould asked, “What hope can then be offered to the flesh and blood amidst the slings and arrows of such outrageous fortune?”
Dr. Briggs said in an interview that scientists for some time have suspected that “we were just not finding the right deposits and only seeing a small piece of the picture of what was going on in life back then.”
For that reason, Dr. Briggs said, he expected other scientists would be less surprised by the discovery than reassured. The fossil record for a long stretch after the Middle Cambrian may be spotty and minimal, but has not vanished. The Moroccan fossils not only reveal the continuation of many Cambrian life forms, he said, but show “the high potential that there are other places for finding these Cambrian-like organisms persisting in time.”
As a consequence, the discovery team wrote, the Moroccan sediments offer promising links between the Cambrian Explosion of multicellular life, exemplified in the Burgess Shale, and the early stages of what is known as the Great Ordovician Biodiversification Event, which is considered “one of the most dramatic episodes in the history of marine life.”
This led to the emergence of fish about 400 million years ago and the migration of four-limbed vertebrates from water onto land 360 million years ago. After the catastrophic mass extinction at the end of the Permian period, about 250 million years ago, the dinosaurs came to the fore in a reptilian world, and after their extinction 65 million years ago, mammals came into their own, hominids evolving probably less than 8 million years ago, modern humans less than 200,000 years ago.
That any of these early Ordovician remains endured verges on the miraculous. Some with shells could be expected to fossilize, but most of these were soft-bodied creatures, prone to rapid decay. The Moroccan fossil beds, Dr. Briggs noted, were once the muddy bottom of an ocean. Storms stirred up the seabed, burying doomed creatures safe from scavengers and in recesses with little or no oxygen to promote decomposition. The sediment chemistry transformed iron and sulfide into pyrite, which coated and preserved the shapes of the animals, including their appendages, and mineralized internal tissue.
“The exquisite preservation of the soft anatomy,” Dr. Van Roy said, “allows more complete, accurate reconstructions of their genetic affinities and ecology than has hitherto been possible.”
Hard at work last week in the Moroccan fossil beds, Dr. Van Roy said, “I obviously intend to exploit this fantastic research opportunity to the fullest.”
Life in the Third Realm
By OLIVIA JUDSON, The New York Times, MAY 18, 2010
It’s that time of the month again. Yes: it’s time for Life-form of the Month. In case you’ve forgotten, this coming Saturday is International Day for Biological Diversity, a day of celebrations and parties to appreciate the other occupants of the planet. So if you do nothing else this weekend, drink a toast to “Other Life-forms!” In honor of this event, my nomination for Life-form of the Month: May is a group of abundant and fascinating beings that are undeservedly obscure: the archaea.
Say who?
Archaea are single-celled microbes with a reputation for living in tough environments like salt lakes, deep sea vents or boiling acid. One strain can grow at temperatures as high as 121 degrees Celsius (249.8 degrees Fahrenheit), a heat that kills most organisms; others thrive at the seriously acidic pH of zero.
They are not restricted to life at the fringes, however. As we have learned how to detect them, archaea have turned up all over the place. One survey estimated that they account for as much as 20 percent of all microbial cells in the ocean, and they’ve been discovered living in soil, swamps, streams and lakes, sediments at the bottom of the ocean, and so on. They are also routinely found in the bowels of the Earth — and the bowels of animals, including humans, cows and termites, where they produce methane. Indeed, the archaeon known as Methanobrevibacter smithii may account for as much as 10 percent of all the microbial cells living in your gut.
But here’s the thing. The tree of life falls into three big lineages, or realms of life. (Confession: the technical term is “domains,” not “realms,” but I’m taking poetic license.) The most familiar realm comprises the eukaryotes — which is the blanket term for most of the organisms we are familiar with, be they mushrooms, water lilies, tsetse flies, humans or the single-celled beasties that cause malaria. Eukaryotes have many distinguishing features, including the fact that they keep their genes in a special compartment known as the cell nucleus.
The second member of the trinity is made up of bacteria. We tend to associate bacteria with disease — for they can cause a range of nasty infections, including pneumonia, syphilis, leprosy, tuberculosis and the like. But in fact, most bacteria lead blameless lives (some of which I have written about in previous columns). There are many differences between eukaryotes and bacteria; but one of the most obvious is that bacteria do not sequester their DNA in a cell nucleus.
Courtesy NASA/JPL-Caltech Methanogens, a type of archaea.
The third great lineage of living beings is the archaea. At first glance, they look like bacteria — and were initially presumed to be so. In fact, some scientists still classify them as bacteria; but most now consider that there are enough differences between archaea and bacteria for the archaea to count as a separate realm.
The most prominent of these differences lies in the structure of the ribosome — the piece of cellular machinery that is responsible for turning the information contained in DNA into proteins. Indeed, it was the discovery of the archaeal ribosome by the biologist Carl Woese in the 1970s that led to their being recognized as the third branch of the tree of life.
What else sets them apart? They sometimes come in peculiar shapes: Haloquadratum walsbyi is rectangular, for example. Some archaea are ultra-tiny, with cell volumes around 0.009 cubic microns. (For comparison, human red blood cells have a volume of around 90 cubic microns. A micron is a millionth of a meter — which is extremely small.)
More diagnostic: archaeal cell membranes have a different structure and composition from those of bacteria or eukaryotes. And although archaea organize their DNA much as bacteria do (they also have no cell nucleus, for example), many aspects of the way the DNA gets processed are distinctly different. Instead, the processing is more similar to what goes in within eukaryotic cells. Archaea also have large numbers of genes that are not found in the other groups.
But to me their most telling feature is that they have their own set of extremely weird viruses. Not only do archaeal viruses also come in odd shapes — some of them look like little bottles — but the set of genes they have is unlike that of viruses that parasitize bacteria or eukaryotes. In other words, viruses can also be divided into three big groups: those that attack bacteria, those that attack eukaryotes and those that attack archaea.
The archaea still hold many mysteries. Few of them can be grown in the laboratory, so they are hard to study in detail; many of them are known from their DNA alone. Moreover, their exact position on the tree of life — when they evolved relative to the other two groups — remains disputed. Yet it may be that archaea feature in our ancestry: according to one view, eukaryotes themselves evolved from an ancient fusion between a bacterium and an archaeon.
But whether this is the case, or whether they are merely co-occupants of the planet, let’s hear it for these Other Life-forms!
Notes:
For a delightful introduction to the archaea, see Howland, J. L. 2000. “The Surprising Archaea: Discovering Another Domain of Life.” Oxford University Press. For a more technical overview, see Cavicchioli, R. (editor). 2007. “Archaea: Molecular and Cellular Biology.” ASM Press. See page 21 for a photograph of the square archaeon, Haloquadratum walsbyi; this book also contains detailed descriptions of how archaea differ from eukaryotes and bacteria.
For archaea thriving at temperatures of 121 degrees C, see Kashefi, K. and Lovley, D. R. 2003. “Extending the upper temperature limit for life.” Science 301: 934. For archaea growing at zero pH, see Fütterer, O. et al. 2004. “Genome sequence of Picrophilus torridus and its implications for life around pH 0.” Proceedings of the National Academy of Sciences USA 101: 9091-9096.
For an overview of places where archaea have been found, see Chaban, B., Ng, S. Y. M., and Jarrell, K. F. 2006. “Archaeal habitats—from the extreme to the ordinary.” Canadian Journal of Microbiology 52: 73-116. For archaeal residents of animal guts, see Lange, M., Westermann, P., and Ahring, B. K. 2005. “Archaea in protozoa and metazoa.” Applied Microbiology and Biotechnology 66: 465-474. For archaea comprising 20 percent of ocean microbes, see DeLong, E. and Pace, N. R. 2001. “Environmental diversity of bacteria and archaea.” Systematic Biology 50: 470-478. For Methanobrevibacter smithii comprising 10 percent of the human gut microbial population, see Samuel, B. S. et al. 2007. “Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.” Proceedings of the National Academy of Sciences USA 104: 10643-10648.
Descriptions of eukaryotes and bacteria can be found in any general biology textbook. For the view that archaea are merely a type of exotic bacteria, see page 123 of Cavalier-Smith, T. 2010. “Deep phylogeny, ancestral groups and the four ages of life.” Philosophical Transactions of the Royal Society B 365: 111-132. For a robust account of the three branches view of the tree of life, see for example, Pace, N. R. 2009. “Mapping the tree of life: progress and prospects.” Microbiology and Molecular Biology Reviews 73: 565-576.
For ultra-tiny archaea (and for the volume of 0.009 cubic microns), see Baker, B. J. et al. 2010. “Enigmatic, ultrasmall, uncultivated Archaea.” Proceedings of the National Academy of Sciences USA 107: 8806-8811. I took the volume of the human red blood cell from table 1 of Gregory, T. R. 2000. “Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals.” Genome 43: 895-901.
For the bizarre features of archaeal viruses, see Prangishvili, D., Forterre, P. and Garrett, R. A. 2006. “Viruses of the Archaea: a unifying view.” Nature Reviews Microbiology 4: 837-848. The origin of eukaryotes, and whether it involved the fusion between a bacterium and an archaeon, is much disputed. See, for example, Yutin, N. et al. 2008. “The deep archaeal roots of eukaryotes.” Molecular Biology and Evolution 25: 1619-1630; Kurland, C. G., Collins, L. J., and Penny, D. 2006. “Genomics and the irreducible nature of eukaryotic cells.” Science 312: 1011-1014; and Hartman, H. and Fedorov, A. 2002. “The origin of the eukaryotic cell: a genomic investigation.” Proceedings of the National Academy of Sciences USA 99: 1420-1425.
Many thanks to Jonathan Swire for insights, comments and suggestions.
High-Tech Tour of the Caves of Nottingham
By SINDYA N. BHANOO, The New York Times, May 17, 2010
Legend has it that Robin Hood was captured by the Sheriff of Nottingham and then imprisoned in the sandstone caves that lie beneath the city.
Whether Robin Hood was real or mythological is debatable, but the caves of Nottingham, carved into soft sandstone, do exist. Throughout the city, under modern day homes and businesses and the Nottingham Castle, there is a labyrinth of medieval tunnels, dungeons and cellars. Now, using laser technology, researchers are collecting 500,000 data points a second, measuring the size and scope of the caves at a pace that was not previously possible.
The result is a chance to create an archaeological record of the caves, and create a 3D model that visitors can explore on the Internet. The researchers are producing sweeping, color animated views of the caves that users can zoom in and out of and crawl through, just as they might in a real cave.
“We’re trying to produce these flights through videos and images — to open up not only caves that are publicly accessible, but also those that might be under private ownership, for people who can’t visit the caves physically,” said David Walker, an archaeologist at the University of Nottingham who is leading the project.
Another goal is to create a mobile phone application that lets users learn about the caves while taking a self-guided walking tour of the city.
Dr. Walker visits the caves himself, collecting data points that he later pieces together in his lab. One of the more remarkable visits was to a 14th-century dungeon where carvings of the 12 Apostles were found in the walls.
The $370,000, two year project was started in February and is financed by the city of Nottingham, the University of Nottingham and philanthropic donations.
By GINA KOLATA, The New York Times, May 17, 2010
At the Boston Marathon last month, my running partner, Jen Davis, said things were pretty much the same as the 10 other times she has run this race. Most runners stood around waiting for the race to start. Some did strides — short bursts of speed — or ran briefly at close to their race pace. There was a lot of stretching, too, and applications of heat rubs like Bengay and jumping up and down to stay warm.
My son, Stefan Kolata, was with the elite men this year in Boston and warmed up with them in their own special pre-race area. Those runners had a very different routine, he says. They spent about 15 minutes doing sort of a slow shuffle. There they were, a long line of elites, going around and around the warm-up area, barely lifting their legs.
Then, some went to a parking lot and did dynamic stretching — high knees, backward running, sideways running. Others vanished from the outdoor warm-up area, emerging again when the race was about to begin.
When it was all over, the men’s winner finished in 2:05:52, an average pace of 4 minutes 48 seconds per mile. Even the 10th-place finisher had a time of 2:10:33, or 4:59 a mile. So maybe these fast men know a secret about warm-ups.
Or maybe not.
Just about every serious competitive athlete, it seems, warms up before a race or even a training session. But there seems to be no particular method to their warm-ups.
Some, like Paula Radcliffe, the world record holder for the women’s marathon, spend more time warming up than most people spend running.
“Warm-up usually takes 45 to 50 minutes and is pretty much the same for workouts and races,” she told me. It consists of jogging for 10 to 20 minutes, stretching, and then doing strides.
But her warm-up is short and easy compared with the cyclist Andy Hampsten’s 90-minute warm-up before a time trial, in which cyclists ride one by one as fast as they can over a course that is typically about 25 miles.
Mr. Hampsten, who rode in the Tour de France and was the only American ever to win the Tour of Italy, began his warm-up with 30 minutes of easy riding followed by 40 minutes in which he rode as hard as he could for intervals of 2 minutes, alternating with 5 minutes at an easy pace, followed by 20 more minutes of easy riding. He said he knew he was warmed up when he got “a mild endorphin buzz.”
At the other extreme is the Olympic swimmer Dara Torres.
“I don’t need a ton of warm-up to be ready for my races,” she said. Her warm-up is just “some light swimming, kicking and drills,” followed by a few sprints.
Exercise researchers say they are not surprised by the lack of consensus on warming up. There is a theory of why it should improve performance, but there is dearth of good research on whether it actually does.
The theory, said Paul Laursen, a performance physiologist at the Millennium Institute of Sport and Health, in Auckland, New Zealand, is that muscles contract better after they have already been contracting.
As a muscle warms up, the force of its contractions can be charted like a staircase: when it starts to work, the contractions may be only half as strong as they are after it has contracted a few times. The explanation is that the contractions release calcium ions in the cells, enabling the muscle fibers to contract more forcefully. At the same time, muscle enzymes, which work best when slightly higher than body temperature, heat up and become more efficient.
That may be why the elite male marathoners did well after their slow shuffles. “Despite the fact that they can go so fast,” Dr. Laursen said, it will take only a few muscle contractions for their muscles to warm up effectively for their long duration event.”
But the story may be different for shorter events. Dr. Laursen said that athletes might do best with a high-intensity warm-up, the sort that Andy Hampsten did; that can allow fast-twitch muscle fibers to contract more efficiently and can prepare the nerve fibers and the cardiovascular system for an all-out effort.
That, at least, is the theory. What’s missing is evidence showing actual effects on performance.
There’s almost nothing credible, as Andrea J. Fradkin an exercise researcher at Bloomsburg University of Pennsylvania, discovered when she searched for published studies on warm-ups. Most of the research was done in the 1960s and ’70s, she told me, and its quality was poor.
In a recent review article she wrote, “Many of the earlier studies were poorly controlled, contained few study participants and often omitted statistical analysis.”
The studies were of so little value, she concluded, that “it is not known whether warming up is of benefit, of potential harm, or having no effect on an individual’s performance.”
An exception is Dr. Fradkin’s own studies of warming up before playing golf. After a decade of research, she found that a seven-and-a-half-minute warm-up involving cardiovascular exercise, stretching and air swings — swinging a golf club without hitting a ball — can significantly improve performance.
But that does not necessarily mean the same routine will work in other sports. As Dr. Fradkin put it, “How can you compare improving performance in golf with improving performance in swimming?”
It’s an appalling situation, she told me. Serious athletes place so much emphasis on warming up, yet what they do is based more on trial and error than on science. For now, she said, what to do “is almost a ‘he said, she said’ thing.”
Creatures of Cambrian May Have Lived On
By JOHN NOBLE WILFORD, The New York Times, May 17, 2010
Ever since their discovery in 1909, the spectacular Burgess Shale outcrops in the Canadian Rockies have presented scientists with a cornucopia of evidence for the “explosion” of complex, multicellular life beginning some 550 million years ago.
The fossils, all new to science, were at first seen as little more than amazing curiosities from a time when life, except for bacteria and algae, was confined to the sea — and what is now Canada was just south of the Equator. In the last half century, however, paleontologists recognized that the Burgess Shale exemplified the radiation of diverse life forms unlike anything in earlier time. Here was evolution in action, organisms over time responding to changing fortunes through natural experimentation in new body forms and different ecological niches.
But the fossil record then goes dark: the Cambrian-period innovations in life appeared to have few clear descendants. Many scientists thought that the likely explanation for this mysterious disappearance was that a major extinction had wiped out much of the distinctive Cambrian life. It seemed that the complex organisms emerging in the Cambrian had come to an abrupt demise, disappearing with few traces in the later fossil record.
Not everyone was convinced, however, and now a trove of 480-million-year-old fossils in Morocco appears to strike a blow to the idea of a major extinction. The international team of scientists who discovered the 1,500 fossils said their find shows that the dark stretch in the fossil record more probably reflects an absence of preservation of fossils over the previous 25 million years.
The team reports in the current issue of the journal Nature that the large number of “exceptionally preserved” Moroccan species exhibits apparently strong links to Cambrian species known from fossil beds in China, Greenland and, most notably, the Burgess Shale. The scientists think this solves the mystery. The Moroccan fossils, they said, establish that Burgess Shale-type species “continued to have an important role in the diversity and ecological structure of deeper marine communities well after the Middle Cambrian.”
The Moroccan fossils include sponges, worms, trilobites and mollusks like clams, snails and relatives of the living nautilus. Another fossil was similar to today’s horseshoe crab, a biological throwback familiar to beachcombers. Now, the scientists said, its antiquity appears to be even greater — some 30 million years earlier than previously thought, possibly in the late Cambrian.
The discovery team’s principal scientist and lead author of the journal article was Peter Van Roy, a Belgian paleontologist who is a postdoctoral fellow at Yale University. He has worked in Moroccan fossil beds the last 10 years, but it was only last year on a field trip, financed by the National Geographic Society, that he and other scientists uncovered the riches of a site near the Atlas Mountains and the city of Zagora.
Scientists from Britain, France, Ireland, Morocco and the United States participated in the research and were co-authors of the team report. A local fossil collector, Mohammed Ou Said Ben Moulal, directed Dr. Van Roy to the rock outcrops he had scouted.
Soon it became clear, Dr. Van Roy said last week in an e-mail message from Morocco, that the team had “really discovered the whole gamut of these Burgess animals, the majority of which had never been found after the Middle Cambrian.”
A leading member of the team, Derek E. G. Briggs, director of the Peabody Museum of Natural History at Yale, cut his academic teeth studying the Burgess Shale. Dr. Briggs figured prominently in “Wonderful Life: The Burgess Shale and the Nature of History,” the 1989 book by Stephen Jay Gould about what the author called the “weird wonders” of the Cambrian period.
In the book, Dr. Gould, who died in 2002, pondered the mystery of the relatively sudden burst of new life designs in the Cambrian, followed by their apparent disappearance. “What turned it off so quickly?” he asked. A few pages before, quoting Charles Darwin, he seemed to despair of finding the fossils to answer the question.
“Darwin wrote,” Dr. Gould recalled, “that our imperfect fossil record is like a book preserving just a few pages, of these pages few lines, of the lines few words, and of those words few letters.”
Darwin’s metaphor pertained to the chances of preservation for bones and teeth. So referring to the predominance of soft-body anatomies of Cambrian life, Dr. Gould asked, “What hope can then be offered to the flesh and blood amidst the slings and arrows of such outrageous fortune?”
Dr. Briggs said in an interview that scientists for some time have suspected that “we were just not finding the right deposits and only seeing a small piece of the picture of what was going on in life back then.”
For that reason, Dr. Briggs said, he expected other scientists would be less surprised by the discovery than reassured. The fossil record for a long stretch after the Middle Cambrian may be spotty and minimal, but has not vanished. The Moroccan fossils not only reveal the continuation of many Cambrian life forms, he said, but show “the high potential that there are other places for finding these Cambrian-like organisms persisting in time.”
As a consequence, the discovery team wrote, the Moroccan sediments offer promising links between the Cambrian Explosion of multicellular life, exemplified in the Burgess Shale, and the early stages of what is known as the Great Ordovician Biodiversification Event, which is considered “one of the most dramatic episodes in the history of marine life.”
This led to the emergence of fish about 400 million years ago and the migration of four-limbed vertebrates from water onto land 360 million years ago. After the catastrophic mass extinction at the end of the Permian period, about 250 million years ago, the dinosaurs came to the fore in a reptilian world, and after their extinction 65 million years ago, mammals came into their own, hominids evolving probably less than 8 million years ago, modern humans less than 200,000 years ago.
That any of these early Ordovician remains endured verges on the miraculous. Some with shells could be expected to fossilize, but most of these were soft-bodied creatures, prone to rapid decay. The Moroccan fossil beds, Dr. Briggs noted, were once the muddy bottom of an ocean. Storms stirred up the seabed, burying doomed creatures safe from scavengers and in recesses with little or no oxygen to promote decomposition. The sediment chemistry transformed iron and sulfide into pyrite, which coated and preserved the shapes of the animals, including their appendages, and mineralized internal tissue.
“The exquisite preservation of the soft anatomy,” Dr. Van Roy said, “allows more complete, accurate reconstructions of their genetic affinities and ecology than has hitherto been possible.”
Hard at work last week in the Moroccan fossil beds, Dr. Van Roy said, “I obviously intend to exploit this fantastic research opportunity to the fullest.”
Life in the Third Realm
By OLIVIA JUDSON, The New York Times, MAY 18, 2010
It’s that time of the month again. Yes: it’s time for Life-form of the Month. In case you’ve forgotten, this coming Saturday is International Day for Biological Diversity, a day of celebrations and parties to appreciate the other occupants of the planet. So if you do nothing else this weekend, drink a toast to “Other Life-forms!” In honor of this event, my nomination for Life-form of the Month: May is a group of abundant and fascinating beings that are undeservedly obscure: the archaea.
Say who?
Archaea are single-celled microbes with a reputation for living in tough environments like salt lakes, deep sea vents or boiling acid. One strain can grow at temperatures as high as 121 degrees Celsius (249.8 degrees Fahrenheit), a heat that kills most organisms; others thrive at the seriously acidic pH of zero.
They are not restricted to life at the fringes, however. As we have learned how to detect them, archaea have turned up all over the place. One survey estimated that they account for as much as 20 percent of all microbial cells in the ocean, and they’ve been discovered living in soil, swamps, streams and lakes, sediments at the bottom of the ocean, and so on. They are also routinely found in the bowels of the Earth — and the bowels of animals, including humans, cows and termites, where they produce methane. Indeed, the archaeon known as Methanobrevibacter smithii may account for as much as 10 percent of all the microbial cells living in your gut.
But here’s the thing. The tree of life falls into three big lineages, or realms of life. (Confession: the technical term is “domains,” not “realms,” but I’m taking poetic license.) The most familiar realm comprises the eukaryotes — which is the blanket term for most of the organisms we are familiar with, be they mushrooms, water lilies, tsetse flies, humans or the single-celled beasties that cause malaria. Eukaryotes have many distinguishing features, including the fact that they keep their genes in a special compartment known as the cell nucleus.
The second member of the trinity is made up of bacteria. We tend to associate bacteria with disease — for they can cause a range of nasty infections, including pneumonia, syphilis, leprosy, tuberculosis and the like. But in fact, most bacteria lead blameless lives (some of which I have written about in previous columns). There are many differences between eukaryotes and bacteria; but one of the most obvious is that bacteria do not sequester their DNA in a cell nucleus.
Courtesy NASA/JPL-Caltech Methanogens, a type of archaea.
The third great lineage of living beings is the archaea. At first glance, they look like bacteria — and were initially presumed to be so. In fact, some scientists still classify them as bacteria; but most now consider that there are enough differences between archaea and bacteria for the archaea to count as a separate realm.
The most prominent of these differences lies in the structure of the ribosome — the piece of cellular machinery that is responsible for turning the information contained in DNA into proteins. Indeed, it was the discovery of the archaeal ribosome by the biologist Carl Woese in the 1970s that led to their being recognized as the third branch of the tree of life.
What else sets them apart? They sometimes come in peculiar shapes: Haloquadratum walsbyi is rectangular, for example. Some archaea are ultra-tiny, with cell volumes around 0.009 cubic microns. (For comparison, human red blood cells have a volume of around 90 cubic microns. A micron is a millionth of a meter — which is extremely small.)
More diagnostic: archaeal cell membranes have a different structure and composition from those of bacteria or eukaryotes. And although archaea organize their DNA much as bacteria do (they also have no cell nucleus, for example), many aspects of the way the DNA gets processed are distinctly different. Instead, the processing is more similar to what goes in within eukaryotic cells. Archaea also have large numbers of genes that are not found in the other groups.
But to me their most telling feature is that they have their own set of extremely weird viruses. Not only do archaeal viruses also come in odd shapes — some of them look like little bottles — but the set of genes they have is unlike that of viruses that parasitize bacteria or eukaryotes. In other words, viruses can also be divided into three big groups: those that attack bacteria, those that attack eukaryotes and those that attack archaea.
The archaea still hold many mysteries. Few of them can be grown in the laboratory, so they are hard to study in detail; many of them are known from their DNA alone. Moreover, their exact position on the tree of life — when they evolved relative to the other two groups — remains disputed. Yet it may be that archaea feature in our ancestry: according to one view, eukaryotes themselves evolved from an ancient fusion between a bacterium and an archaeon.
But whether this is the case, or whether they are merely co-occupants of the planet, let’s hear it for these Other Life-forms!
Notes:
For a delightful introduction to the archaea, see Howland, J. L. 2000. “The Surprising Archaea: Discovering Another Domain of Life.” Oxford University Press. For a more technical overview, see Cavicchioli, R. (editor). 2007. “Archaea: Molecular and Cellular Biology.” ASM Press. See page 21 for a photograph of the square archaeon, Haloquadratum walsbyi; this book also contains detailed descriptions of how archaea differ from eukaryotes and bacteria.
For archaea thriving at temperatures of 121 degrees C, see Kashefi, K. and Lovley, D. R. 2003. “Extending the upper temperature limit for life.” Science 301: 934. For archaea growing at zero pH, see Fütterer, O. et al. 2004. “Genome sequence of Picrophilus torridus and its implications for life around pH 0.” Proceedings of the National Academy of Sciences USA 101: 9091-9096.
For an overview of places where archaea have been found, see Chaban, B., Ng, S. Y. M., and Jarrell, K. F. 2006. “Archaeal habitats—from the extreme to the ordinary.” Canadian Journal of Microbiology 52: 73-116. For archaeal residents of animal guts, see Lange, M., Westermann, P., and Ahring, B. K. 2005. “Archaea in protozoa and metazoa.” Applied Microbiology and Biotechnology 66: 465-474. For archaea comprising 20 percent of ocean microbes, see DeLong, E. and Pace, N. R. 2001. “Environmental diversity of bacteria and archaea.” Systematic Biology 50: 470-478. For Methanobrevibacter smithii comprising 10 percent of the human gut microbial population, see Samuel, B. S. et al. 2007. “Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.” Proceedings of the National Academy of Sciences USA 104: 10643-10648.
Descriptions of eukaryotes and bacteria can be found in any general biology textbook. For the view that archaea are merely a type of exotic bacteria, see page 123 of Cavalier-Smith, T. 2010. “Deep phylogeny, ancestral groups and the four ages of life.” Philosophical Transactions of the Royal Society B 365: 111-132. For a robust account of the three branches view of the tree of life, see for example, Pace, N. R. 2009. “Mapping the tree of life: progress and prospects.” Microbiology and Molecular Biology Reviews 73: 565-576.
For ultra-tiny archaea (and for the volume of 0.009 cubic microns), see Baker, B. J. et al. 2010. “Enigmatic, ultrasmall, uncultivated Archaea.” Proceedings of the National Academy of Sciences USA 107: 8806-8811. I took the volume of the human red blood cell from table 1 of Gregory, T. R. 2000. “Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals.” Genome 43: 895-901.
For the bizarre features of archaeal viruses, see Prangishvili, D., Forterre, P. and Garrett, R. A. 2006. “Viruses of the Archaea: a unifying view.” Nature Reviews Microbiology 4: 837-848. The origin of eukaryotes, and whether it involved the fusion between a bacterium and an archaeon, is much disputed. See, for example, Yutin, N. et al. 2008. “The deep archaeal roots of eukaryotes.” Molecular Biology and Evolution 25: 1619-1630; Kurland, C. G., Collins, L. J., and Penny, D. 2006. “Genomics and the irreducible nature of eukaryotic cells.” Science 312: 1011-1014; and Hartman, H. and Fedorov, A. 2002. “The origin of the eukaryotic cell: a genomic investigation.” Proceedings of the National Academy of Sciences USA 99: 1420-1425.
Many thanks to Jonathan Swire for insights, comments and suggestions.
High-Tech Tour of the Caves of Nottingham
By SINDYA N. BHANOO, The New York Times, May 17, 2010
Legend has it that Robin Hood was captured by the Sheriff of Nottingham and then imprisoned in the sandstone caves that lie beneath the city.
Whether Robin Hood was real or mythological is debatable, but the caves of Nottingham, carved into soft sandstone, do exist. Throughout the city, under modern day homes and businesses and the Nottingham Castle, there is a labyrinth of medieval tunnels, dungeons and cellars. Now, using laser technology, researchers are collecting 500,000 data points a second, measuring the size and scope of the caves at a pace that was not previously possible.
The result is a chance to create an archaeological record of the caves, and create a 3D model that visitors can explore on the Internet. The researchers are producing sweeping, color animated views of the caves that users can zoom in and out of and crawl through, just as they might in a real cave.
“We’re trying to produce these flights through videos and images — to open up not only caves that are publicly accessible, but also those that might be under private ownership, for people who can’t visit the caves physically,” said David Walker, an archaeologist at the University of Nottingham who is leading the project.
Another goal is to create a mobile phone application that lets users learn about the caves while taking a self-guided walking tour of the city.
Dr. Walker visits the caves himself, collecting data points that he later pieces together in his lab. One of the more remarkable visits was to a 14th-century dungeon where carvings of the 12 Apostles were found in the walls.
The $370,000, two year project was started in February and is financed by the city of Nottingham, the University of Nottingham and philanthropic donations.
