Published: The New York Times, May 13, 2010

FOR centuries, speculation about the existence of life elsewhere in the universe was the preserve of philosophers and theologians. Then, 50 years ago last month, the question entered the scientific sphere when a young American astronomer named Frank Drake began sweeping the skies with a radio telescope in hopes of picking up a signal from an extraterrestrial civilization. Initially, his quest was considered somewhat eccentric. But now the pendulum of scientific opinion has swung to the point where even a scientist of the stature of Stephen Hawking is speculating that aliens exist in other parts of our galaxy.

The search for extraterrestrial intelligence is predicated on the assumption, widely held today, that life would emerge readily on Earth-like planets. Given that there could be upward of a billion Earth-like planets in our galaxy alone, this assumption suggests that the universe should be teeming with life.

But the notion of life as a cosmic imperative is not backed up by hard evidence. In fact, the mechanism of life’s origin remains shrouded in mystery. So how can we test the idea that the transition from nonlife to life is simple enough to happen repeatedly? The most obvious and straightforward way is to search for a second form of life on Earth. No planet is more Earth-like than Earth itself, so if the path to life is easy, then life should have started up many times over right here.

Searching for alternative life on Earth might seem misconceived, because there is excellent evidence that every kind of life so far studied evolved from a common ancestor that lived billions of years ago. Yet most of the life that exists on Earth has never been properly classified. The vast majority of species are microbes, invisible to the naked eye, and scientists have analyzed only a tiny fraction of them. For all we know, there could be microbes with other ancestral origins living literally under our noses — or even inside our noses — constituting a sort of shadow biosphere, containing life, but not as we know it.

The denizens of the hidden “alien” biosphere — let’s call them Life 2.0 — might employ radically different biochemical processes than the life we know and love. Microbiologists could easily have overlooked their existence, because their methods are focused on the biochemistry of standard life. Obviously, if you go looking for A, you will find A and not B.

One way to go about tracking down Life 2.0 is to make educated guesses about what its biochemistry might be like. Alternative microbes might, for example, have different chemical elements. One shrewd suggestion, made by Felisa Wolfe-Simon of the United States Geological Survey, is that phosphorus — crucial to life as we know it — could be replaced by arsenic. She and her colleague Ron Oremland are dredging bugs from arsenic-contaminated Mono Lake in California in search of arsenic life.

Other researchers are focusing on the handedness of molecules. In standard life, the key amino acids are always left-handed, and the sugars are right-handed. Scientists are not sure why standard life has made this particular choice; nonliving chemical mixtures tend to contain equal amounts of both left- and right-handed molecules.

If life started again, perhaps it would select different handedness for its key molecules. Should a shadow biosphere of “mirror microbes” exist, the organisms could be identified by culturing microbial samples in “mirror soup” — a cocktail of nutrients with the handedness reversed, available from commercial suppliers. Standard life would find the soup unpalatable, but mirror life would thrive on it. Some experiments along these lines are being carried out at NASA’s Marshall Space Flight Center, in Huntsville. Ala.

Life 2.0 would be easier to identify if it inhabited distinct niches beyond the reach of regular life. Microbes are known to dwell in the superheated water around volcanic vents in the deep ocean, for example. Others survive extremes of cold, salinity, acidity or radiation. Yet all these so-called extremophiles that have been investigated to date are the same life as you and me. Regular life is clearly very hardy and adaptable, and can tolerate amazingly harsh conditions. Nevertheless, there will be limits. If Life 2.0 has a different chemical constitution, it may lurk in pockets at even more extreme temperatures or higher levels of radiation.

An argument often given for why Earth couldn’t host another form of life is that once the life we know became established, it would have eliminated any competition through natural selection. But if another form of life were confined to its own niche, there would be little direct competition with regular life. And, in any case, natural selection doesn’t always mean winner-takes-all. Some years ago it was discovered that simple microbes actually belong to two very distinct domains — bacteria and archaea. Genetically, these groups differ from each other as much as they differ from humans. Yet they have peacefully co-existed in overlapping habitats for billions of years.

If my theory turns out to be correct, it will have sweeping consequences. Should we find a second form of life right here on our doorstep, we could be confident that life is a truly cosmic phenomenon. If so, there may well be sentient beings somewhere in the galaxy wondering, as do we, if they are not alone in the universe.

Paul Davies, the director of the Beyond Center for Fundamental Concepts in Science at Arizona State University, is the author of “The Eerie Silence: Renewing Our Search for Alien Intelligence.”

On May 16, 1960, Hughes Lab researcher Theodore Maiman became the first person on earth to build a laser. Fifty years later, the technology is now one of the most ubiquitous on the planet.  Photo: Raytheon

The name LASER is an acronym for Light Amplification by the Stimulated Emission of Radiation. In 1917, Albert Einstein first theorized about the process which makes lasers possible called “Stimulated Emission.”  This past Sunday, the laser was 50 years old.

The process which makes lasers possible, Stimulated Emission, was proposed in 1917 by Albert Einstein. No one realized the incredible potential of this concept until the 1950’s, when practical research was first performed on applying the theory of stimulated emission to making lasers. It wasn’t until 1960 that the first true laser was made by Theodore Maimam, out of synthetic ruby. Many ideas for laser applications quickly followed, including some that never worked, like the laser eraser. Still, the early pioneers of laser technology would be shocked and amazed to see the multitude of ways that lasers are used by everyone, everyday, in today’s world.

In 1954, Charles Townes and Arthur Schawlow invented the maser (microwave amplification by stimulated emission of radiation), using ammonia gas and microwave radiation – the maser was invented before the (optical) laser. The technology is very close but does not use a visible light.

On March 24, 1959, Charles Townes and Arthur Schawlow were granted a patent for the maser. The maser was used to amplify radio signals and as an ultrasensitive detector for space research.

The pinpoint beam of a laser can focus precisely on a target and make highly delicate incisions. This new found precision achieved by using lasers has drastically changed modern medicine. High precision operations are now made possible thanks to lasers.

Pulsed lasers remove the worry of damaging surrounding tissue. An individual pulse of light lasting 5 billionths of a second will remove only 0.2 microns of eye tissue. This is just one hundredth of the diameter of a typical cell. This type of precise tissue removal can be used to sculpt eye tissue alleviating the common sight problem of near-sightedness.

A similar technique will remove electrons from molecules, leaving behind a collection of charged particles known as a plasma. This plasma can absorb laser energy and become larger, creating a shock-wave that disrupts the material around it. This technique is used to remove cataracts from the eye.

Removing red birthmarks known as Port-Wine stains was one of the first applications of laser technology to medicine. The red mark results from hundreds of extra blood vessels that lie beneath the outer surface of the skin. These blood vessels selectively absorb light of the blue or green wavelengths that an argon laser emits. Thus, the argon laser beam can selectively heat the blood vessels, essentially burning them away, without too much damage to the surrounding skin. A similar technique is used to treat the excessive growth of blood vessels in the retina that occurs in Diabetic Retinopathy.

The laser is able to reach organs inside the body through a related technology known as fiber optics. Laser light passes through extremely thin hollow tubes without losing intensity or changing color. Optical fibers can be inserted into natural or surgically created holes in the body. Light can be received through one fiber and transmitted through another. This way a doctor can both see the problem and effect it.

For instance, a small hole in the stomach can be made with a laser incision. An optical fiber is inserted to reach the gallbladder. A long pulse laser is used to cut out the diseased gallbladder from the surrounding liver tissue, sealing the surrounding blood vessels to avoid excess bleeding. Then, the doctor can attempt to pull the gallbladder out of the hole. Sometimes the gallbladder is so ladden with hard mineral deposits (gallstones) that it doesn’t fit through the hole. To remedy this, the doctor can hit the stones with a pulsed laser that causes a shock wave in the gallstones, breaking them apart. This procedure illustrates how different elements of laser technology are used in medicine.

Doctor Steven Trokel patented the Excimer laser for vision correction. The Excimer laser was originally used for etching silicone computer chips in the 1970s. IBM researchers saw, in 1982, the potential of the Excimer laser in interacting with biological tissue. The IBM team realized that you could remove tissue with a laser without causing any heat damage to the neighboring material.

New York City ophthalmologist, Steven Trokel made the connection to the cornea and performed the first laser surgery on a patient’s eyes in 1987. The next ten years were spent perfecting the equipment and the techniques used in laser eye surgery. In 1996, the first Excimer laser for ophthalmic refractive use was approved in the United States.

Lasers make fantastic rulers. They measure distances with incredible accuracy. There are two major ways a laser can do this. One way a laser can measure distance is by time of flight. The other method is called interferometry.

To measure a distance using time of flight, shoot a laser beam at an object and wait until it returns to the location of the laser. The speed that photons travel in air is constant for all photons – about 670 million miles per hour. Because we know the constant speed of light, it is possible to determine distances by bouncing a laser beam off a target and measuring the time it takes to return.

Time of flight technolgy can be used to measure widely varying distances. Hand held laser rulers can measure the length of a room. Light detection and ranging, or LIDAR, can determine satellite positions, the shape of the Earth’s surface and properties of the Earth’s atmosphere.

The other method is called interferometry. Interferometry relies on the nature of light to travel in waves. Wavelengths of photons interfere with each other making crests or troughs much like waves in water do. The wave pattern of two beams of laser light hitting each other tells you about the difference in distance the two light beams had to travel. Interferometry can measure very small distances, around the size a wavelength of light.

Interferometry is used in industry to make highly accurate measurements of the size of tiny, delicate instrument parts. It was also important historically with Einstein’s formulation of the Theory of Relativity.

Medical experts say there are no easy answers. For now, their best advice is for women to ask that their breast cancer tissue be sent to experienced labs that follow accreditation procedures like those recommended by the College of American Pathologists


The New York Times, May 17, 2010, by Gina Kolata  –  Dr. Linda Griffith was at a conference in Singapore in early January when she felt a lump in her breast. She assumed it was nothing — a cyst. And anyway, she had no time for it. She was returning on a Sunday night and the next Tuesday morning was leaving for a conference in Florida.

But she had a mammogram, ultrasound and biopsy within hours of getting off the plane. The news was not good: she had cancer.

Then the complications began. Dr. Griffith, director of the Center for Gynepathology Research at M.I.T., had a test to see whether her tumor had extra copies of a protein, HER2. If it did, it would respond to a drug, Herceptin, which blocks the protein and stymies the tumor’s growth.

Drugs aimed at disabling proteins that spur cancer are, many oncologists say, the future of cancer therapies. Only a few are available now but almost every new drug under study is designed to disable cancer-fueling proteins.

But these so-called targeted therapies are only as good as tests to find their protein targets. And while most patients do not yet know it, those tests can be surprisingly unreliable.

Acknowledging the problem, cancer specialists on Monday announced new testing guidelines for one protein target, but as new targets are identified, the problem continues to grow.

The test on Dr. Griffith’s tumor was negative. Or was it? One small area of her tumor stained chocolate brown, indicating lots of HER2. The rest was a cream color, indicating no extra HER2 protein.

Yet her treatment hinged on this result. A HER2 positive tumor has a bad prognosis. Herceptin can make that prognosis good, reducing the chances that the cancer will come back by 50 percent and reducing a woman’s risk of dying by 40 percent.

But Herceptin, costing $42,000 a year wholesale, causes flulike symptoms and also has a rare, serious side effect, severe heart damage that can even be fatal.

And if a tumor does not have high levels of HER2, Herceptin would be, as Dr. Antonio Wolff, a breast cancer specialist at Johns Hopkins put it, “a toxic and expensive placebo.”

Dr. Griffith had come face to face with an emerging, but rarely acknowledged, problem in today’s era of new cancer tests and therapies.

HER2 tests, for instance, can give false-positives up to 20 percent of the time, wrongly telling women they need the drug when they do not. Five percent to 10 percent of the time the tests can falsely tell a woman that she should not take the drug, when she should. And Herceptin testing for breast cancer is easy compared with what is coming next.

Genentech, Herceptin’s maker, is about to apply to the Food and Drug Administration to sell the drug to treat stomach cancer. But it is much more difficult to tell whether a stomach tumor has high levels of HER2, said Krysta Pellegrino, a company spokeswoman. Breast cancers usually are all positive or all negative. Not stomach cancers, which almost always have sections that are positive for HER2 and sections that are negative. The HER2 tests are the same, but “the interpretation and scoring are different,” Ms. Pellegrino said.

That sort of mosaic pattern is typical of cancers other than breast cancer, says Dr. Jeffrey Bloss, vice president, North America Medical Affairs at GlaxoSmithKline. And it raises questions of what a test result means.

“The science is still evolving,” Dr. Bloss said. “What was true last year may not be true this year.”

Like the HER2 tests, other molecular tests for breast cancer also have problems. Those tests, for estrogen receptors on breast cancer cells, determine whether cancer will be thwarted by drugs that deprive tumors of estrogen. They can be wrong at least 10 percent of the time. Some estrogen-depleting drugs, while generally safe, increase the risk of osteoporosis and, depending on the drug, can also cause joint pain and increase risks of stroke and cancer of the uterine lining.

Estrogen receptor tests are a muddle, noted Dr. Edith Perez, a breast cancer specialist at the Mayo Clinic in Jacksonville, Fla. Quite a few tests are being used, but Dr. Perez could not ascertain exactly how many or how good they were in predicting whether a tumor would respond to estrogen-depleting drugs.

And different labs may do tests in different ways; some even invent their own.

“How do you know they are the same?” Dr. Perez asked. “If you do the test in two different labs, you can get two different answers.”

Error rates for newer tests have not even been established.

“This is an issue that transcends breast cancer,” Dr. Wolff said. “A poorly developed test is potentially as dangerous as a poorly developed drug.”

The Food and Drug Administration says it is concerned about the quality of tests developed by clinical laboratories for their own use, said Alberto Gutierrez, who oversees diagnostic products for the agency. Some of the tests are increasingly complex, Mr. Gutierrez said, adding that there is a proliferation of laboratories offering tests without F.D.A. oversight. But, for now, the agency has no specific plan to regulate the tests, in part because of lack of money.

Meanwhile, Dr. Griffith’s doctor, Eric Winer at the Dana-Farber Cancer Institute, had a gradual awakening.

“In my naïve view, which wasn’t so many years ago,” Dr. Winer said, “I thought HER2 was a switch that turns on or off and it was pretty easy to tell when it’s on or off. It turns out that it is not nearly as straightforward for a large number of tumors.”

Now, recognizing the problem, Dr. Winer had Dr. Griffith’s tumor retested with a different method, hoping the result would help him and Dr. Griffith figure out whether she could benefit from Herceptin.

And Dr. Griffith was left facing the uncertainties of cancer medicine.

“Me as a scientist says it’s very interesting,” she said.

But, she said, as a patient she sees it differently.

“It’s really hard to know what to do,” Dr. Griffith said.

The two large national studies of Herceptin for women with HER2 positive early-stage breast cancer were just starting in 2001 when Dr. Perez, of the Mayo Clinic, a principal investigator, had a moment of truth. Women were having HER2 tests at a variety of places — community hospitals, major medical centers, national labs. Dr. Perez decided to retest tumors in a central lab to confirm the results.

The outcome stunned her and her colleagues. Twenty percent of the first 119 women whose initial tests indicated their tumors had excess HER2 turned out not to have it on retesting.

“We all felt, ‘Oh boy, we have a problem,’ ” said Dr. Wolff, a study investigator. “This was huge.”

So the studies were modified to require central labs to retest all the tumors.

Yet the discordance remained — one-sixth of women told by local labs that they were HER2 positive were not on retesting.

“We were all horrified,” said Dr. Elizabeth Hammond, a pathologist at Intermountain HealthCare in Utah.

The result of that moment of horror was HER2 testing guidelines by the College of American Pathology and the American Society of Clinical Oncology, dictating criteria for declaring a test positive or negative and requiring proficiency testing, among other things.

In a way, the effort was a huge success. About 900 of the nation’s estimated 1,500 labs agreed to follow the guidelines.

But even so, said Dr. Bloss of GlaxoSmithKline, there seemed to be approximately a 20 percent discordance between labs. GlaxoSmithKline makes Tykerb, which also focuses on HER2.

There are all sorts of reasons why different labs can get different results, said Dr. Mitch Dowsett of the Royal Marsden Hospital in London and a member of the United States committee that formulated HER2 testing guidelines.

In borderline cases, pathologists can disagree. Or stain can pool in areas where a tumor was crushed or damaged, making it look, to inexperienced eyes, like a positive stain.

Twelve years after Herceptin was approved for women with advanced breast cancer, “we’re still trying to refine the testing,” said Ms. Pellegrino of Genentech.

Then there is Dr. Griffith’s problem: what to do when part of a tumor is positive and the rest is negative.

The College of American Pathologists wants to develop testing guidelines for every molecular target for cancer drugs. On Monday, for example, ASCO and CAP released new guidelines for estrogen receptor testing.

And Dr. Hammond has become driven to make sure pathologists know about and follow the HER2 guidelines.

At pathology meetings, she asks her audience how many know about the guidelines and are following them.

“Almost everyone raises their hand,” Dr. Hammond said. “I am preaching to the choir. They chose to come to the meeting. It’s the ones who did not choose to come that I am worried about.”

But even the best labs can differ, as some women learned.

When Sheila Maloney had breast cancer surgery in October, her doctor wanted to test her tumor for HER2.

“I had never heard of it,” said Mrs. Maloney, a 64-year-old hostess at an Olive Garden restaurant in Lady Lake, Fla.

She is now seeing Dr. Perez, and ended up having her tumor tested four times with four different commonly used HER2 tests. The first test was positive, the second negative, the third positive, the fourth negative.

Dr. Perez recommended that Mrs. Maloney take Herceptin.

As for Dr. Griffith, the two tests for HER2 turned out to agree, but with that mixed result, it was hard to know what to do. Her tumor was on the fence — part negative, part weakly positive.

Medical experts say there are no easy answers. For now, their best advice is for women to ask that their breast cancer tissue be sent to experienced labs that follow accreditation procedures like those recommended by the College of American Pathologists.

But Dr. Griffith did all that. And Dr. Griffith, a scientist whose own research involves the HER2 protein, also read and examined the literature on HER2 to prepare for a discussion with Dr. Winer.

“Here I sit as a patient. My situation is ambiguous,” Dr. Griffith said.

In the end, the studies, along with Dr. Winer’s clinical perspective, did not convince her that the drug would help. The risk of serious heart damage and other side effects was scary. And, she said, she cannot ignore the drug’s price, even though her insurer would pay.

Dr. Griffith decided not to take Herceptin, but she is having standard chemotherapy.

“I am very comfortable with my decision,” she said., May 17, 2010  –  NEW YORK–People who have lost some or all of their adult teeth typically look to dentures, or more recently, dental implants to bridge the gap between a toothless appearance.

But this appearance can have a host of unsettling psycho-social ramifications and a tooth-filled grin that is not without pain and discomfort.

Despite being the preferred treatment for missing teeth today, dental implants can fail and have no ability to “remodel” with surrounding jaw bone, which undergoes necessary and unavoidable changes throughout a person’s life.

But a new technique pioneered in the Tissue Engineering and Regenerative Medicine Laboratory of Dr. Jeremy Mao, Edward V. Zegarelli Professor of Dental Medicine, and a professor of biomedical engineering at Columbia University, can orchestrate the body’s stem cells to migrate to three-dimensional scaffold that is infused with growth factor. This can yield an anatomically correct tooth in as soon as nine weeks once implanted in the mouth.

“These findings represent the first report of regeneration of anatomically shaped tooth-like structures in vivo,  and by cell homing without cell delivery,” Dr. Mao and his colleagues said in the paper.

“The potency of cell homing is substantiated not only by cell recruitment into scaffold microchannels, but also by regeneration of a putative periodontal ligaments newly formed alveolar bone.”

Dental implants usually consist of a cone-shaped titanium screw with a roughened or smooth surface and are placed in the jaw bone. While implant surgery may be performed as an outpatient procedure, healing times vary widely and successful implantation is a result of multiple visits to certified clinicians, including general dentists, oral surgeons, prosthodontists and periodontists.

Implant patients must allow two to six months for healing and if the implant is installed too soon, it is possible that the implant may move which results in failure. The subsequent time to heal, graft and eventually place a new implant may take up to 18 months.

The work of Dr. Mao and his laboratory, however, holds manifold promise: a more natural process, faster recovery times, and a harnessing of the body’s potential to regrow tissue that will not give out and could ultimately last the patient’s lifetime.

By homing stem cells to a scaffold made of natural materials and integrated in surrounding tissue, there is no need to use harvested stem cell lines, or create a an environment outside of the body (e.g., a Petri dish) where the tooth is grown and then implanted once it has matured.

The tooth instead can be grown “orthotopically,” or in the socket where the tooth will integrate with surrounding tissue in ways that are impossible with hard metals or other materials.

“A key consideration in tooth regeneration is finding a cost-effective approach that can translate into therapies for patients who cannot afford or who aren’t good candidates for dental implants,” Dr. Mao said. “Cell-homing-based tooth regeneration may provide a tangible pathway toward clinical translation.”

This study is published in the Journal of Dental Research, a top journal in the field of dentistry.

This research was supported by NIH ARRA Funding via 5RC2 DE020767 from the National Institute of Dental and Craniofacial Research.

For more information, visit

To read more about dental implants, go to

To comment on this topic, go to


DentistryIQ, May17, 2010, by Greg Lynch  –  Even discriminating sushi connoisseurs would envy the tuna George Amato has sampled. The purpose of the tasty experiment: Use DNA barcoding to find out if threatened species of tuna are sold in the United States market.

Barcoding relies on a short fragment of mitochondrial DNA found in virtually all living things. The 650 base-pair region, part of the cytochrome oxidase I (COI) gene, accumulated mutations at a high rate during evolution, and can now be used to distinguish between many related species of animals or insects. “It’s one of the best species identifiers,” says Amato, director of the American Museum of Natural History’s Sackler Institute for Comparative Genomics. “Although tuna barcodes are a little more tricky.”

That’s because species of tuna are closely related, so their barcodes show little variation. While Amato has used barcodes to distinguish threatened gorillas, sea turtles, and crocodiles from their common relatives, researchers have debated whether the technique could be applied to tuna.

To answer this question, Amato’s graduate student set up a couple of dinner dates. PhD candidate Jake Lowenstein ordered tuna from 31 high-end restaurants and neighborhood sushi bars in New York City and Denver, then placed meat samples in a test tube. “Many of the meals were paid for by the supportive people who accompanied Jake to dinner,” jokes Amato. More than $2,000 was spent on 68 samples.

Back at the lab, the DNA extraction and sequencing processes went smoothly, but identifying the fish took more innovation. Scientists usually search indexes like GenBank and the Barcode of Life Database to match mystery meat sequences to known species. “We look to match the barcode sequence we get from our meat sample with at least 98 percent similarity,” says Amato. “The problem is that tuna are already right at this cut off.” While species of parrots, sharks, and other animals vary by 4–10 percent, a bluefin tuna may only differ from an albacore by 2 percent. This makes it hard to distinguish them.

One-third of the purchased tuna was threatened; seven samples were critically endangered species.

To get around this problem, the team set statistical comparisons aside and began searching within the barcode for sites that characterized each species. “We had known samples of tuna, and were able to show that southern bluefin (Thunnus maccoyii) had unique identifying sites,” says Amato.

Northern bluefin (T. thynnus), yellowfin (T. albacares), albacore (T. alalunga) and other tuna could also be recognized by subsections of their DNA barcode. This allowed the team to conclusively identify the restaurant samples.

It turns out that one-third of the purchased tuna was threatened, including Northern and Pacific bluefin, which have both declined by more than 90 percent since the 1970s. Seven samples were identified as the critically endangered southern bluefin, which currently faces extinction.

While conservation groups warn consumers against ordering threatened tuna, the findings show this is easier said than done. More than half of the menus misrepresented the species name, calling threatened Northern and Southern bluefin “fatty tuna” or “tuna.” Other times, restaurants got the species name entirely wrong. Some samples were not even tuna, but escolar (Lepidocybium flavobrunneum)—a fish banned for sale in Italy and Japan for causing stomach upset. (PLoS ONE 4(11): e7866, 2009.)

The findings mark a bright future for a controversial technology. “The ability to easily identify specimens of the species in international trade with an existing tool would be helpful,” says David Morgan, Chief of the Scientific Support Unit at The Convention on the International Trade of Endangered Species (CITES).

This March, CITES delegates voted against a Northern bluefin trade ban, although protections may be introduced by fishery management organizations.

In the meantime, US regulators can tackle the misidentification of tuna on menus, says Amato. This spring, he will train Customs and Boarder Protection scientists to find fraudulent fish and other endangered meats. “As a museum we can’t prosecute consumer fraud, but barcoding can help regulatory agencies address the problem,” he says.

While taxonomists debate whether barcoding should be used for classifying new species, critics are warming up to its uses in the meat trade. “For species discrimination, barcodes don’t always work properly,” says Karina Lucas of the Piracicaba, Brazil-based Escola Superior de Agricultura “Luiz de Queiroz.” “But we think barcodes could be very useful in cases of partially processed meat and seafood.”

Read more: Catch of the day – The Scientist – Magazine of the Life Sciences

A red grouper rests in its excavated hole.
Courtesy of NOAA Underwater Research Program / University of North Carolina, Wilmington

It was 2 o’clock in the morning, and marine scientist Felicia Coleman, floating 150 kilometers offshore of the gulf coast of Tampa, Fla., was growing weary of looking at a monitor. It was displaying live images being captured by the remotely operated vehicle (ROV) some 90 meters below, showing lots of rock clusters inside holes in the seafloor, but nothing to explain how the holes got there. Then Coleman saw something unexpected—red grouper sweeping rocks from the seafloor holes they call home with their tail fins.

“It was one of those moments [that] you see these cartoons where scientists are yelling, ‘Eureka! I’ve found it!’” recalls Coleman, based at Florida State University. “It woke us up.” Watching the video stream, the researchers started to get the sense that the grouper were actively digging the holes, creating this habitat for themselves and the other fish. They had gone out to see what species were living in this newly protected habitat, and ended up finding something that was actually building it. “We got pretty giddy about it,” she says.

Coleman was anxious to learn more, but studying anything 90 meters below the surface was no easy task. Then she learned that juvenile red grouper live in just a few meters of water all along the Florida Keys.

First, Coleman and her team identified holes that were still full of sediment, and placed juvenile red groupers in open-bottomed cages over the filled-in holes. Donning her SCUBA gear, she dropped to the seafloor to observe the fish gulping up the sediment into their mouths and dumping it at the perimeter of the cage. Within 48 hours, each hole had been sufficiently excavated to allow the juvenile fish to fit comfortably inside of it (Open Fish Sci J, 3:1–15, 2010).

These excavations do more than simply hollow out a home for a single, predatory fish. Spiny lobster, for example, which draw tens of thousands of fishers to the Gulf each year, tend to rest inside the holes during the day before heading out on their nightly hunting escapades. Furthermore, many sessile invertebrate species settle on the rock substrate exposed by grouper excavation, attracting even more organisms, such as cleaner shrimp that nestle among the tentacles of the excavation-associated anemone. Thus conservation efforts that target the red grouper, which are currently the most commonly fished grouper species in the Gulf of Mexico, could protect other marine species as well.

Groupers Dig It

In fact, Coleman found that biodiversity increased significantly with the size of the excavated area, and decreased considerably as she looked farther and farther away from the holes. “The wonderful thing about this study is it shows that red grouper are important in their ecosystems in a way that beavers are in their ecosystems,” says marine ecologist Elliott Norse of the Marine Conservation Biology Institute. “They’re keystone habitat modifiers or ecosystem engineers.”

“We know that biodiversity is really important for ecosystem function—the higher the biodiversity, the better the recovery, and the less collapse you get in a fishery” following large harvests, says marine ecologist Susan Williams of the University of California at Davis. Thus, such ecosystem engineers are “very good targets” for management strategies. “If you protect them, you’re protecting a [whole] suite of species.”

Red grouper aren’t the only piscine architects. Gobies, for example, dig little holes in the sand, which in turn attract cleaner shrimp and other fish. And on a larger scale, tile fish are famous for the pueblo-like structures they build along the slop of the continental shelf.

But red grouper are “another clear example of how ecosystem engineers are important components of marine ecosystems,” says Hunter Lenihan of University of California, Santa Barbara, “and how we should try to focus attention on their management and their sustainability.”

Read more: Aquatic Architects – The Scientist – Magazine of the Life Sciences