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Category Archives: Transhuman News

Illumina’s DNA Supercomputer Heralds the $1,000 Human Genome

Posted: January 14, 2014 at 10:46 pm

The $1,000 human genome is here. For real this time.

Illumina (ILMN), the worlds leading seller of gene sequencing machines, unveiled its HiSeq X (pronounced High Seek 10) on Tuesday. The system is the worlds first DNA-crunching supercomputer designed to process 20,000 genomes per year at a cost of $1,000 each. Currently it costs about $10,000 to sequence a human genome. Jay Flatley, Illuminas chief executive officer, introduced the machine at an investors conference in San Francisco, saying customers will begin receiving the machine this quarter. This will be a blockbuster product, he said in an interview.

The biotech industry has been trying to reach the $1,000 genome mark for years. Its a figure that should make full genome sequencing much more mainstream. As more people get sequenced, researchers get more data to use in their analysis of how DNA variations manifest themselves in diseases. The high-speed, low-cost sequencing system arrives at a crucial time, with a number of biotech companies, research centers, and hospitals starting to show real clinical breakthroughs. To figure out cancer, we need to sequence hundreds of thousands of cancer genomes, and this is the way to do it, Flatley said.

About a decade ago it cost much more than $1 billion to sequence a human genome, and the process took months. Illuminas new machine can knock out dozens of genomes in about a day. The HiSeq X systems, which cost $1 million each, should end up at large research centers and will be sold in groups of 10. Illumina has unveiled a smaller, $250,000 system called the NextSeq 500, which can fit on a laboratory counter and handle one genome at a time. The first customers for the HiSeq X include Macrogen, the Broad Institute in Cambridge, Mass., and the Garvan Institute of Medical Research in Sydney.

If it feels like weve been through this whole $1,000 genome thing before, its because we have. In early 2012, Ion Torrent, which was acquired by Life Technologies (LIFE), declared victory, saying it had a machine capable of the $1,000 genome in hand. The celebration, however, was premature. Glitches have prevented the company from actually selling such a machine. We expect it to be out in 2014, says Ron Andrews, the president of genetic and medical sciences at Life. We still have a team working on it, but it is not the ultimate goal. I think the reality is there are bigger and more urgent business opportunities than the $1,000 genome.

Illumina, based in San Diego, has fended off dozens of startups that were meant to upend the sequencing market and make its machines obsolete. In 2011, for example, Pacific Biosciences (PACB) began selling a machine (that cost $600million to design) with the promise to sequence genomes faster and more accurately than ever before. The system has not lived up to its billing, as its mostly been used for highly specialized botanical sequencing and for some cancer genomes that have repetitive sequences which are tough for other machines to decipher. According to a recent survey by industry trade publication In Sequence, Illumina increased its market share to 71 percent during 2013, followed by Life at 16percent, Roche (RHO:GR) at 10percent, and PacBio at 3percent. Wall Street analysts expect Illumina to report revenue of about $1.6billion this year, according to data compiled by Bloomberg.

Along with holding off startups, Illumina has had to contend with a hostile takeover attempt from Roche and Chinas recent entry into the sequencing-machine market. From late 2011 through the early part of 2012, Roche tried to acquire Illumina, topping out its bids at $51 per share. According to Flatley, Illuminas board was reluctant to sell, knowing it had these new machines and the potential for growth on the way. Illumina went so far as to prepare a roadshow in which it would show off its upcoming systems to convince investors about the possibility of a bright future. It was our responsibility to let the shareholders know what was in the kitchen being cooked, Flatley says. Ultimately, Illumina fended off the bid and kept the systems secret. Its share price has since surged, trading today at $117 per share.

Flatley says Illumina will continue to reduce the cost of sequencing hardware, as well as diversify into services. Last year, for example, it acquired Verinata Health for about $350 million. Verinata performs tests for expecting parents to see if their children have any chromosomal abnormalities; it does so via a blood test rather than the dreaded amniocentesis procedure. Illumina also offers a human genome sequencing service, which comes with a complimentary MyGenome app for the iPad, and has moved into cancer diagnostics.

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Illumina's DNA Supercomputer Heralds the $1,000 Human Genome

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Does Illumina Have the First $1,000 Genome?

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Illumina announces a new high-end sequencer made for factory-scale sequencing of human genomes.

Humans only: A new high-throughput sequencing machine from Illumina is optimized to sequence thousands of human genomes in a year.

The $1,000 genome has been a catchphrase of the sequencing industry for years, but despite bold promises from different companies, this benchmark hasnt been met. Now, thanks to a new sequencing machine from Illumina, it may finally be within reach.

At the J.P. Morgan Healthcare Conference on Tuesday, Illumina CEO Jay Flatley announced a new high-end sequencing machine that could accurately sequence whole human genomes at a cost of less than $1,000 each. Competitor Ion Torrent (later bought by Life Technologies) announced in 2012 that it had developed a machine capable of doing so (see Device Brings $1,000 Genome Within Reach), but capability has yet to materialize. Illuminas new machine is scheduled to reach its first customers in March. Faster chemistry and better opticsIlluminas machines read DNA sequences by analyzing patterns of fluorescent nucleotideshave allowed costs to come down.

The $1,000 price tag is often seen as vital to making whole-genome sequencing cost-effective for medical testing and personalized medicine. At this price, it might become reasonable for well-off patients to have their genomes sequenced for potential medical information.

Still, Illuminas new machines will be out of reach for most labs. The ultrahigh-throughput sequencers will be sold in systems of at least 10 machines each, at a starting price of $10 million. According to Flatley, the $1,000 price tag does take into account the cost of the machines, chemicals to do each run of sequencing, sample prep, and more. But these are machines intended to sequence tens of thousands of genomes each year.

Illumina emphasizes that the new machines will speed population-level genome sequencing for large projects aimed at understanding human disease and natural genetic variation. In his presentation, Flatley predicted an explosion of demand for factory-scale sequencing of human genomes. He pointed to a few large-scale projects already in the works, including the U.S. Veterans Affairs project to sequence the genomes of thousands of former soldiers and the U.K.s 100K Genomes project, which will sequence the genomes of National Health Service patients to help guide their care and to study genetic disease (see Why the U.K. Wants a Genomic National Health Service).

Researchers still struggle to understand how changes in DNA sequence cause disease and influence health. Large-scale sequencing projects can help reveal associations between a particular DNA variant and a disease or a healthy outcome. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine, said Eric Lander, founding director of the MIT and Harvard genomics center the Broad Institute, in a released statement.

The Illumina machine was built specifically for human genomes, says Flatley, and it can sequence human genomes accurately enough to reliably identify DNA variants 10 times faster than its predecessor, another high-end Illumina machine. While other machines may sequence human genomes more quickly, they cannot produce the same quality of sequence data at that speed, says Joel Fellis, a senior manager of product marketing at Illumina.

Flatley says the new machine can partially sequence five human genomes in a day. A complete run takes three days, during which time it can produce 16 human genomes at a quality level widely accepted by the sequencing community.

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Does Illumina Have the First $1,000 Genome?

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Illumina breaks genome cost barrier

Posted: at 10:46 pm

SAN FRANCISCO The cost of sequencing a human genome has been brought below $1,000, San Diego DNA sequencing giant Illumina said Tuesday, opening the door to bringing the full benefit of 21st-century genomic medicine to the public.

The lower cost is made possible by the new HiSeq X Ten Sequencing System, announced by Illumina chief executive Jay Flatley at the JP Morgan Healthcare Conference in San Francisco.

Bringing the price below $1,000 is like breaking the sound barrier, Flatley said. That cost level long has been considered the price below which mass adoption of genome sequencing becomes feasible.

There was a collective gasp that went across the room, said Joe Panetta, chief executive of Biocom, the San Diego-based life science trade group.

Illuminas announcement was a big surprise, said Dr. Eric Topol, a pioneer in health care genomics and chief academic officer of Scripps Health in San Diego. Topol said genome sequencing costs appeared to have been stuck around the $3,000 to $5,000 range for a couple of years.

Knowledge of a persons individual genetic makeup helps doctors find out which drugs work best and what diseases they may be predisposed to get. Studying many genomes helps advance research by allowing individual variations to be linked to health. On a larger scale, more efficient treatment holds the promise of reining in rising health care costs by making medicine more effective.

Genome sequencing costs have been plummeting since the first genome was sequenced about 13 years ago, for a price in the hundreds of millions. Lower costs have allowed more exploration of the differences between individuals. These differences are the key to the goal of providing individualized health care.

But while the cost of genome sequencing has fallen to mass-market levels, the machines that perform them are far most costly. So these machines will mostly appeal to research laboratories and large health systems that can use them on a big scale.

The $1,000 cost takes into account the cost of the machines and the chemicals needed to do the sequencing, but not overhead, Flatley said. Interpreting the genome readout is not part of the process; trained scientists and clinicians must determine what the sequence means.

Illuminas new system consists of 10 HiSeq X sequencing machines, which sell for $1 million each, bringing the total system cost to $10 million. The new system will start shipping in March, Flatley said.

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Illumina breaks genome cost barrier

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San Diego Company Claims Major Milestone In Gene Sequencing

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Photo by DOE Joint Genome Institute

Above: Older Illumina machines put the price of sequencing a genome around $10,000.

Sequencing an entire genome for $1,000 or less has long been seen as a tipping point in the field of genetics. At $1,000 a pop, sequencing would be within reach for many patients. And scientists studying the roll of genes in cancer and other diseases could greatly expand their research.

One San Diego company says they've now succeeded in bringing prices down that low.

Illumina CEO Jay Flatley announced the price cut today at the JP Morgan Healthcare Conference in San Francisco. The San Diego-based leader in gene sequencing claims to be the first company to reach this major milestone.

"It has come as a surprise," said Kelly Frazer, director of the Institute of Genomic Medicine at UC San Diego. She says researchers in her field knew the thousand-dollar genome was coming soonbut maybe not this soon.

Describing Illumina's new sequencers as "breakout technology," Frazer said, "It's going to mean a lot for basic researchers doing human disease work. And there's a potential for it to mean a lot for the clinic also."

The system itself is fairly expensive. At $10 million, the machines included in Illumina's HiSeq X Ten package are targeted towards large research institutions for now.

Though it could be awhile before typical patients see the benefits of a $1,000 genome, Frazer said the impact on her own research could be great. Her lab has been studying genetic risk factors for venous thromboembolism (VTE), a disease that causes potentially deadly blood clots.

To stay within budget, Frazer currently relies on incomplete genetic snapshots of her 1,2000 subjects. She says a $1,000 genome would allow her to order full sequencing for an even larger cohort, giving her a better idea of who might be at risk for VTE.

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San Diego Company Claims Major Milestone In Gene Sequencing

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Humans burn only half the calories daily

Posted: at 10:46 pm

New York, Jan 14 (IANS): In a discovery that can lead to new understanding about human health and longevity, researchers have found that humans and other primates burn 50 percent fewer calories each day than other mammals. Humans, chimpanzees, baboons and other primates expend only half the calories we would expect for a mammal.

To put that in perspective, a human - even someone with a very physically active lifestyle - would need to run a marathon each day just to approach the average daily energy expenditure of a mammal their size, said Herman Pontzer, an anthropologist at Hunter College in New York and the lead author of the study.

These remarkably slow metabolisms explain why humans and other primates grow up so slowly and live such long lives.

Most mammals, like the family dog, live a fast-paced life, reaching adulthood in a matter of months, reproducing prodigiously and dying in their teens if not well before.

By comparison, humans and our primate relatives (apes, monkeys, lorises, and lemurs) have long childhoods, reproduce infrequently, and live exceptionally long lives, said the study published in the journal Proceedings of the National Academy of Sciences.

Scientists examined daily energy expenditure in 17 primate species - from gorillas to mouse lemurs - to test whether primates' slow pace of life results from a slow metabolism.

Using a safe and non-invasive technique known as 'doubly labeled water', - which tracks the body's production of carbon dioxide - the researchers measured the number of calories that primates burned over a 10-day period.

The results were a real surprise. This dramatic reduction in metabolic rate, previously unknown for primates, accounts for their slow pace of life, said Pontzer.

The research also sheds light on the fact that zoo-housed primates are relatively active, with the same daily energy expenditures as wild primates, said co-author Steve Ross from Chicago's Lincoln Park Zoo.

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Humans burn only half the calories daily

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Primate growing up with half the calories: New understanding about human health and longevity

Posted: at 10:46 pm

Jan. 13, 2014 New research shows that humans and other primates burn 50% fewer calories each day than other mammals. The study, published January 13 in the Proceedings of the National Academy of Sciences, suggests that these remarkably slow metabolisms explain why humans and other primates grow up so slowly and live such long lives. The study also reports that primates in zoos expend as much energy as those in the wild, suggesting that physical activity may have less of an impact on daily energy expenditure than is often thought.

Most mammals, like the family dog or pet hamster, live a fast-paced life, reaching adulthood in a matter of months, reproducing prodigiously (if we let them), and dying in their teens if not well before. By comparison, humans and our primate relatives (apes, monkeys, tarsiers, lorises, and lemurs) have long childhoods, reproduce infrequently, and live exceptionally long lives. Primates' slow pace of life has long puzzled biologists because the mechanisms underlying it were unknown.

An international team of scientists working with primates in zoos, sanctuaries, and in the wild examined daily energy expenditure in 17 primate species, from gorillas to mouse lemurs, to test whether primates' slow pace of life results from a slow metabolism. Using a safe and non-invasive technique known as "doubly labeled water," which tracks the body's production of carbon dioxide, the researchers measured the number of calories that primates burned over a 10 day period. Combining these measurements with similar data from other studies, the team compared daily energy expenditure among primates to that of other mammals.

"The results were a real surprise," said Herman Pontzer, an anthropologist at Hunter College in New York and the lead author of the study. "Humans, chimpanzees, baboons, and other primates expend only half the calories we'd expect for a mammal. To put that in perspective, a human -- even someone with a very physically active lifestyle -- would need to run a marathon each day just to approach the average daily energy expenditure of a mammal their size."

This dramatic reduction in metabolic rate, previously unknown for primates, accounts for their slow pace of life. All organisms need energy to grow and reproduce, and energy expenditure can also contribute to aging. The slow rates of growth, reproduction, and aging among primates match their slow rate of energy expenditure, indicating that evolution has acted on metabolic rate to shape primates' distinctly slow lives.

"The environmental conditions favoring reduced energy expenditures may hold a key to understanding why primates, including humans, evolved this slower pace of life," said David Raichlen, an anthropologist at the University of Arizona and a coauthor of the study.

Perhaps just as surprising, the team's measurements show that primates in captivity expend as many calories each day as their wild counterparts. These results speak to the health and well-being of primates in world-class zoos and sanctuaries, and they also suggest that physical activity may contribute less to total energy expenditure than is often thought.

"The completion of this non-invasive study of primate metabolism in zoos and sanctuaries demonstrates the depth of research potential for these settings. It also sheds light on the fact that zoo-housed primates are relatively active, with the same daily energy expenditures as wild primates," said coauthor Steve Ross, Director of the Lester E. Fisher Center for the Study and Conservation of Apes at Chicago's Lincoln Park Zoo. "Dynamic accredited zoo and sanctuary environments represent an alternative to traditional laboratory-based investigations and emphasize the importance of studying animals in more naturalistic conditions."

Results from this study hold intriguing implications for understanding health and longevity in humans. Linking the rate of growth, reproduction, and aging to daily energy expenditure may shed light on the processes by which our bodies develop and age. And unraveling the surprisingly complex relationship between physical activity and daily energy expenditure may improve our understanding of obesity and other metabolic diseases.

More detailed study of energy expenditure, activity, and aging among humans and apes is already underway. "Humans live longer than other apes, and tend to carry more body fat," said Pontzer. "Understanding how human metabolism compares to our closest relatives will help us understand how our bodies evolved, and how to keep them healthy."

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Primate growing up with half the calories: New understanding about human health and longevity

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What is the secret to your longevity?

Posted: at 10:46 pm

Human beings and other primates have an extremely slow metabolism rate. They burn almost 50 percent fewer calories each day than other mammals, which is why they have a longer lifespan, say scientists.

The key to longevity is a slow metabolism rate, say scientists.

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Humans and other primates burn 50 percent fewer calories each day than other mammals and due to their low metabolism rate, they have a longer life span, according to a paper published in the Proceedings of the National Academy of Sciences.

Overall, 17 primate species, such as humans, gorillas, and mouse lemurs were examined for the purpose of the study.

The international group of scientists who carried out the study worked with animals in zoos, sanctuaries in Africa, and in the wild.

Daily energy expenditure of the primates was calculated using a technique called "doubly labeled water," Herman Pontzer, an anthropologist at Hunter College in New York and the lead author of the study, told The Monitor.

Water contains hydrogen and oxygen. Some of the hydrogen and oxygen in the water were being replaced with their variants, also called isotopes, Dr. Pontzer says. After animals drink water, these isotopes would then act as tracers and their presence could be found in their urine. By determining the concentration of isotopes from the urine sample, Pontzer and his team determined how much carbon dioxide the body produced. Over a 10-day period, scientists measured the number of calories primates burned, says Pontzer.

Comparing the results of the experiment with similar data from other studies, the team compared daily energy expenditure among primates to that of other mammals, according to a press release by Chicago's Lincoln Park Zoo. Chimpanzees and gorillasfrom the zoo were examined for the study.

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What is the secret to your longevity?

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Humans, Other Primates Burn Fewer Calories Than Other Mammals

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Posted: Monday, January 13, 2014, 4:00 PM

MONDAY, Jan. 13, 2014 (HealthDay News) -- Humans and other primates burn 50 percent fewer calories a day than other mammals, and this slow metabolism may explain why they grow so slowly and live much longer than other mammals, according to a new study.

Researchers assessed the amount of calories burned per day in 17 primate species ranging from gorillas to mouse lemurs. They lived in zoos, sanctuaries and in the wild.

"The results were a real surprise," study author Herman Pontzer, an anthropologist at Hunter College in New York City, said in a college news release.

"Humans, chimpanzees, baboons, and other primates expend only half the calories we'd expect for a mammal. To put that in perspective, a human -- even someone with a very physically active lifestyle -- would need to run a marathon each day just to approach the average daily energy expenditure of a mammal their size," he explained.

The study also found that primates in captivity burn as many calories a day as those in the wild. This suggests that physical activity may have less of an impact on daily energy expenditure than previously believed, the researchers pointed out.

The findings, published in this week's issue of journal Proceedings of the National Academy of Sciences, could help improve understanding of human health and longevity.

For example, connecting the rate of growth, reproduction and aging to daily energy output may increase knowledge about the processes behind body development and aging. And further investigation into the relationship between physical activity and daily energy expenditure may improve understanding of obesity and other metabolic diseases, according to the researchers.

The investigators are now taking a closer look at energy output, physical activity and aging among humans and apes.

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Humans, Other Primates Burn Fewer Calories Than Other Mammals

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Primates: Now with only half the calories!

Posted: at 10:46 pm

PUBLIC RELEASE DATE:

13-Jan-2014

Contact: Sharon Dewar sdewar@lpzoo.org 312-742-2246 Lincoln Park Zoo

(Chicago Jan. 13, 2014) -- New research shows that humans and other primates burn 50% fewer calories each day than other mammals. The study, published January 13 in the Proceedings of the National Academy of Sciences, suggests that these remarkably slow metabolisms explain why humans and other primates grow up so slowly and live such long lives. The study also reports that primates in zoos expend as much energy as those in the wild, suggesting that physical activity may have less of an impact on daily energy expenditure than is often thought.

Most mammals, like the family dog or pet hamster, live a fast-paced life, reaching adulthood in a matter of months, reproducing prodigiously (if we let them), and dying in their teens if not well before. By comparison, humans and our primate relatives (apes, monkeys, tarsiers, lorises, and lemurs) have long childhoods, reproduce infrequently, and live exceptionally long lives. Primates' slow pace of life has long puzzled biologists because the mechanisms underlying it were unknown.

An international team of scientists working with primates in zoos, sanctuaries, and in the wild examined daily energy expenditure in 17 primate species, from gorillas to mouse lemurs, to test whether primates' slow pace of life results from a slow metabolism. Using a safe and non-invasive technique known as "doubly labeled water," which tracks the body's production of carbon dioxide, the researchers measured the number of calories that primates burned over a 10 day period. Combining these measurements with similar data from other studies, the team compared daily energy expenditure among primates to that of other mammals.

"The results were a real surprise," said Herman Pontzer, an anthropologist at Hunter College in New York and the lead author of the study. "Humans, chimpanzees, baboons, and other primates expend only half the calories we'd expect for a mammal. To put that in perspective, a human even someone with a very physically active lifestyle would need to run a marathon each day just to approach the average daily energy expenditure of a mammal their size."

This dramatic reduction in metabolic rate, previously unknown for primates, accounts for their slow pace of life. All organisms need energy to grow and reproduce, and energy expenditure can also contribute to aging. The slow rates of growth, reproduction, and aging among primates match their slow rate of energy expenditure, indicating that evolution has acted on metabolic rate to shape primates' distinctly slow lives.

"The environmental conditions favoring reduced energy expenditures may hold a key to understanding why primates, including humans, evolved this slower pace of life," said David Raichlen, an anthropologist at the University of Arizona and a coauthor of the study.

Perhaps just as surprising, the team's measurements show that primates in captivity expend as many calories each day as their wild counterparts. These results speak to the health and well-being of primates in world-class zoos and sanctuaries, and they also suggest that physical activity may contribute less to total energy expenditure than is often thought.

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Primates: Now with only half the calories!

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Burning fewer calories: the elixir for longevity

Posted: at 10:46 pm

New research shows that humans and other primates burn 50% fewer calories each day than other mammals. The study, published January 13 in the Proceedings of the National Academy of Sciences, suggests that these remarkably slow metabolisms explain why humans and other primates grow up so slowly and live such long lives. The study also reports that primates in zoos expend as much energy as those in the wild, suggesting that physical activity may have less of an impact on daily energy expenditure than is often thought.

Most mammals, like the family dog or pet hamster, live a fast- paced life, reaching adulthood in a matter of months, reproducing prodigiously (if we let them), and dying in their teens if not well before. By comparison, humans and our primate relatives (apes, monkeys, tarsiers, lorises, and lemurs) have long childhoods, reproduce infrequently, and live exceptionally long lives. Primates' slow pace of life has long puzzled biologists because the mechanisms underlying it were unknown.

An international team of scientists working with primates in zoos, sanctuaries, and in the wild examined daily energy expenditure in 17 primate species, from gorillas to mouse lemurs, to test whether primates' slow pace of life results from a slow metabolism. Using a safe and non-invasive technique known as "doubly labeled water," which tracks the body's production of carbon dioxide, the researchers measured the number of calories that primates burned over a 10-day period. Combining these measurements with similar data from other studies, the team compared daily energy expenditure among primates to that of other mammals.

"The results were a real surprise," said Herman Pontzer, an anthropologist at Hunter College in New York and the lead author of the study. "Humans, chimpanzees, baboons, and other primates expend only half the calories we'd expect for a mammal. To put that in perspective, a human even someone with a very physically active lifestyle would need to run a marathon each day just to approach the average daily energy expenditure of a mammal their size."

This dramatic reduction in metabolic rate, previously unknown for primates, accounts for their slow pace of life. All organisms need energy to grow and reproduce, and energy expenditure can also contribute to aging. The slow rates of growth, reproduction, and aging among primates match their slow rate of energy expenditure, indicating that evolution has acted on metabolic rate to shape primates' distinctly slow lives.

Read more at the Lincoln Park Zoo.

Gorilla image via Shutterstock.

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Burning fewer calories: the elixir for longevity

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