EXPLORING THE BONES

By Pam Eastlick

Welcome to The Deep science and technology column where we cover topics from the deep sea to deep space and beyond.

I discovered this week that the animal file contained a lot of bones and even though it’s not Halloween, I figured we could learn a few things from bones, both the inside and the outside variety. Our first science stories are about the animals with the outside variety. Our first example is an astounding tale of visual memory, but not the kind of visual memory you’re thinking of!

THINKING THE PATTERNS

University of California, Berkeley, graduate student Alistair Boettiger has amassed a beautiful collection of seashells, but not by combing the beach. He created them in his computer. He and George Oster, a UC Berkeley biophysicist, along with University of Pittsburgh mathematical neuroscientist Bard Ermentrout, have written a computer program that generates the complex patterns of seashells using simple principles developed to explain how the brain works and how memories are stored.

The "neural net" model explains how mollusks build their seashells based on the finding that the mollusk’s tongue-like mantle, which overlaps the edge of the growing shell, senses or "tastes" the calcium carbonate layer laid down the day before in order to generate a new layer.

"The pattern on a seashell is the mollusk’s memories," said Oster, a professor of environmental science, and molecular and cell biology. "The shell is laid down in layers, so the mantle is sensing the history of the mollusk’s ‘thoughts’ and extrapolating to the next layer, just like our brains project into the future."

The researchers’ computer model reproduces nearly all known shell shapes, ranging from scallops to whelks, and nearly all the shell patterns that make beachcombing so popular.

To build their model, the scientists first studied electron microscope images of mollusk mantles in order to understand the network of neurons connecting the sensing cells in the mantle with the cells that produce calcium carbonate and proteins – many of them colored pigments – incorporated into the growing shell. Different rates of calcium carbonate secretion determine the shape of the spiral, while different amounts of pigment secretion create a pattern unique to each species.

They then modeled the size and number of the different kinds of neurons that surround the cells that secrete the calcium and pigments using nine different parameters as a neural network that determines how much calcium and pigment is secreted. Using only these nine parameters, the researchers were able to reproduce the shapes and patterns of almost every known sea mollusk.

Interestingly, they found that all shell patterns fall into three basic classes: stripes perpendicular to the growing edge, bands parallel to the growing edge, and complex patterns created by asymmetric "traveling waves" of pigment or calcium deposition.

Striped shells are the easiest to explain with this neural network model. A pigment-secreting cell inhibits secretion of pigment by neighboring cells but not itself, so that the same pattern is repeated day after day, yielding a stripe. Similarly, if one cell pumps up calcium carbonate secretion while depressing secretion by surrounding cells, ridges result. Interestingly, the stripes or ridges split naturally as the shell grows, a mathematical necessity because the size of the inhibition area remains the same as the shell’s edge grows.

Bands parallel to the growing edge can be explained by inhibition of future activity. Pigment secreted on one day can inhibit secreting cells for a few days, resulting in an on/off pattern that produces a series of bands.

The most interesting patterns, however, are waves of activity that interfere to produce zigzags, diamonds, chevrons, arrowheads and a host of other shapes. These come about when a pigment inhibits future secretion at that site but excites secretion in surrounding cells. The pigment thus moves laterally on successive days, producing the equivalent of a traveling wave.

Ironically, most sea snails don’t care a whit about their shell pattern. They are buried in the mud of the seafloor where their patterns are hidden even from potential mates.

This means that the beautiful colors of snail shells aren’t generated for visual reasons and are simply a reflection of the snail’s neural activity. There is no selective pressure to drive the patterns so evolution has explored virtually the entire suite of possible shells.

By adjusting nine parameters in a single equation, a computer model can generate patterned shells (right example in each pair above) that closely resemble real mollusk shells. (Alistair Boettiger/UC Berkeley)

So, a sea shell is a refection of the ‘thoughts’ of the animal that built it. That is a mind-blowing concept. Makes you appreciate that though the snail is ugly, it thinks beautiful thoughts!

Now we move on to another tale of the shell. But first a little aside on kinds of shells. There are several different kinds, but the two most common are bivalve shells and gastropod shells. Bivalves are clams and there are two shells. Gastropod means ‘stomach foot’ and these guys have only one shell. Snails are gastropods and we usually refer to the animal inside any gastropod shell as a snail or snail-like creature.

USING THE AVAILABLE RESOURCES

Deep within the Kairei Indian hydrothermal vent field, two-and-one-half miles below the central Indian Ocean, scientists have discovered a gastropod mollusk, whose armor could improve load-bearing and protective materials in everything from aircraft hulls to sports equipment.

The so-called "scaly-foot gastropod," has a unique tri-layered shell that may hold insights for future mechanical design principles. Specifically, it has a highly calcified inner layer and a thick organic middle layer. But, it’s the extraordinary outer layer fused with granular iron sulfide that excites researchers.

The Kairei Indian vent field is a series of deep gashes in the planet’s surface along a volcanic mountain chain below the Indian Ocean. Hydrothermal vents are basically the throats of volcanoes and they produce high concentrations of sulfides and metals. Researchers have marveled at the concentration of critters of all kinds that have been found living at hydrothermal vents, but this snail is unique because it not only tolerates the poisonous chemicals that leave the vent, it incorporates them into its shell.

In particular, the researchers want to know what advantages the tri-form structure holds for protection against penetrating attacks from predators. Understanding this can give them new ideas for materials that may be used for cars, trucks and military applications.

To test the shell’s properties, researchers performed experiments that simulated generic predatory attacks using both computer models and indentation testing. The indentation testing involved hitting the top of shells with the sharp tip of a probe to measure the shell’s hardness and stiffness.

A number of potential predators were found in the same region as the scaly-foot gastropod. One predator, the cone snail, uses a harpoon-like tooth to inject its victim with paralyzing venom. Additionally, crabs are known to grab gastropods within their claws and attempt to puncture their shells and/or squeeze them, sometimes for days until the mollusks’ shells break.

Their testing led the researchers to the realization that each layer of the scaly-foot’s unique exoskeleton is responsible for a distinct role in mechanical protection. The metal infused outer shell is very resistant to penetration and the organic middle layer allows for energy dissipation and speedy repair of any cracks that may occur in the outer layer. The very firm inner shell gives further resistance to bending and tensile loads.

The researcher fell that the scaly-foot gastropod has very different deformation and protection mechanisms than other gastropods and is more efficient in protection than the typical mollusk.

So . . . .we’ve got deep-sea armor from snails too.

Now we move on to another story of the bones. But this one involves the internal kind and the absolutely bizarre creatures that eat them.

ROOTED IN THE BONE

It sounds like a classic horror story — eyeless, mouthless worms lurk in the dark, settling onto dead animals and sending out green "roots" to devour their bones. In fact, such worms do exist in the deep sea. They were first discovered in 2002 by researchers at the Monterey Bay Aquarium Research Institute (MBARI), who were using a robot submarine to explore Monterey Canyon. But that wasn’t the end of the story. After "planting" several dead whales on the seafloor, a team of biologists recently announced that as many as 15 different species of bone worms may live in Monterey Bay alone.

After years of study, the researchers have begun to piece together the bizarre story of the bone worms, all of which are in the genus Osedax (Latin for, you guessed it, ‘bone eater’). The worms start out as microscopic larvae, drifting through the darkness of the deep sea. At some point they encounter a large dead animal on the seafloor. Following chemical cues, the tiny larvae settle down onto the bones of the dead animal.

Once settled, the bone worms grow quickly. One end of each worm develops feathery palps, which extract oxygen from seawater. The other end of the worm develops root-like appendages that grow into the bone. Bacteria within these roots are believed to digest proteins and perhaps fat within the bones, providing nutrition for the worms.

Soon the worms become sexually mature. Strangely enough, they all become females. Additional microscopic larvae continue to settle in the area. Some of these larvae land on the palps of the female worms. These develop into male worms. But the males never grow large enough to be seen by the naked eye. They find their way into the tube that surrounds the female’s body. Dozens of them share this space, not eating at all, but releasing sperm that fertilize the female’s eggs. Eventually the female worm sends thousands of fertilized eggs out into the surrounding water, and the cycle begins again.

One question the scientists would like answered is how these bone worms manage to find and colonize the bones of dead whales in the vast, pitch-black expanse of the deep seafloor. Between 2004 and 2008, the research team towed five dead whales off of Monterey Bay beaches and sank them at different depths within Monterey Canyon. Every few months, the team would send one of MBARI’s remotely operated vehicles (ROVs) down to study the worms and other animals that had colonized the whale carcasses.

To their surprise, the different whale carcasses yielded different types of bone worms. One whale carcass hosted three or four different types of worms. After examining all of the worms, the researchers concluded that most of them were entirely new to science. They also discovered the worms would colonize cow-bones placed on the seafloor, which showed that the worms were not limited to feeding on dead whales.

Based on their appearance and similarities in their DNA, the researchers divided the bone worms into several groups. Some of the worms have feathery palps, which may be red, pink, striped, or even greenish in color. Others have bare palps. One type of bone worm has no palps at all. Its body forms a single, long, tapering tube, which curls at the end like a pig’s tail. This worm has evolved to live in the seafloor sediment near a dead whale. It sends long, fibrous "roots" into the mud, presumably in search of fragments of bone on which to feed.

Eventually the researchers will give all these new worms their own species names. First, however, they must collect enough samples of each possible species for additional laboratory analysis and distribution to type-specimen collections. Like a classic horror story, the macabre saga of the bone worms will continue to thrill marine biologists for years to come.

This photograph shows a female of an as yet un-named boneworm in the genus Osedax, which has been carefully removed from the whale bone in which it was growing. This worm has feathery palps, which extract oxygen from seawater. At its lower end are an ovisac and bulbous "roots," which would normally be embedded in the whale bone. (Credit: Copyright 2009 Greg Rouse)

The ocean is a strange world indeed.

STORIES OF OURSELVES

By Pam Eastlick

Welcome to The Deep science and technology column where we cover topics from the deep sea to deep space and beyond.

We did animals last week, so I think it’s time we turned our attention to one of the most prevalent animals on the planet; us. No, we’re not THE most prevalent. Discounting the bacteria and other uni-cells (who win hands-down if counted), the most prevalent life form on the planet is probably the insects both in numbers and in mass. But we find it fascinating to study about us so I’ve found some stories about our history that I think you’ll enjoy. And, of course, everybody enjoys a good murder!

THE FIRST MURDER?

Our story begins between 50,000 and 75,000 years ago in a cave in the Zagros Mountains in what is now Iraq. Most of our ancestors lived in caves and in the ’50’s and ’60’s archaeologists found the remains of nine Neanderthals in this cave. One of them called "Shanidar 3," was a 40- to 50-year-old male with signs of arthritis and a sharp, deep slice in his left ninth rib.

The wounded Neanderthal’s rib had apparently started healing before he died. Comparing the wound to medical records from the American Civil War, a time before modern antibiotics, suggested to the researchers that he died within weeks of the injury, perhaps due to associated lung damage from a stabbing or piercing wound.

Researchers have wondered what caused that wound since the man was discovered. Now researchers from Duke University may have come up with an answer. They think he was killed by humans.

Archaeological evidence suggests that by 50,000 years ago humans, but not their Neanderthal cousins, had developed projectile hunting weapons. They used atlatls; spear throwers with detachable handles that connected with darts and spears to effectively lengthen a hurler’s arm and give the missiles a power boost.

As human weapons technology advanced, Neanderthals continued using long thrusting spears in hunting, which they probably tried — for personal safety — to keep between themselves and their prey instead of hurling them. Both Neanderthals and humans were also armed with stone knives. And both species had developed techniques for making sharp stone points.

While examining this Paleolithic cold case, the study’s authors evaluated all the possible causes of the rib wound with the aid of contemporary tools. The injury is "consistent with a number of scenarios, including wounding from a long-range projectile (dart) weapon, knife stab, self-inflicted accidental injury and accidental stabbing by a hunting partner," the report said.

Drawing from studies aimed at improving police and prison guard protection, the researchers concluded that the downward sweep of a knife could have the correct trajectory to produce Shanidar 3’s rib injury. "Knife attacks generally involve a relatively higher kinetic energy," the report said. But the report also states "whatever created that puncture was carrying fairly low kinetic energy at a low momentum. This is consistent with a spear-thrower delivered spear."

The investigators rigged up a special crossbow to fire stone-age projectiles, using calibration marks on the crossbow to tell them how much force they were delivering with each launch. Those tests revealed the delivered energy needed to create similar wounds in the ribs of pig carcasses, which the researchers used as an approximation of a Neanderthal’s body.

The researchers also used measurements from a 2003 study to estimate the impact of using a spear that was thrust instead of thrown, the kind of jabbing that Neanderthals are thought to have used. Thrusting produced higher kinetic energies and caused more massive rib damage than Shanidar 3 sustained.

Another clue was the angle of the wound. Whatever nicked his rib entered the Neanderthal’s body at about 45 degrees downward angle. That’s consistent with the "ballistic trajectory" of a thrown weapon, assuming that Shanidar 3 — who was about 5 feet, 6 inches tall — was standing.

Bottom line? The analysis indicates the wound was made by someone using an atlatl or spear thrower. It appears that at the time Shanidar 3 died, modern humans had atlatls and Neanderthals didn’t. The report states, "We think the best explanation for this injury is a projectile weapon, and given who had those and who didn’t that implies at least one act of inter-species aggression."

So . . . a Paleolithic murder and the first firm evidence that we may have wiped out our cousins. The Neanderthal probably weren’t the first species we wasted and they certainly won’t be the last.

Steven Churchill holds a facsimile Neanderthal spear and an atlatl, a human spear thrower. (Credit: Les Todd)

We’ll travel forward in time and examine another body for some very interesting clues about the origin of one of the most feared diseases in the world.

THE MAN IN THE SEALED TOMB

Israeli archeologists have been examining remains found in a burial cave near Jerusalem. The cave, known as the Tomb of the Shroud, is located in the lower Hinnom Valley and is part of a 1st century cemetery known as Akeldama or ‘Field of Blood’.

One of the first interesting things the scientists discovered is that the man in the tomb didn’t receive a secondary burial. Secondary burials were common practice at the time. The bones were removed after a year and placed in an ossuary (a stone bone box). In this case, however, the entrance to this part of the tomb was completely sealed with plaster.

There was apparently a very good reason for that. The researchers discovered that the man buried in the sealed tomb suffered from leprosy and died of tuberculosis, as the DNA of both diseases was found in his bones. This is the earliest case of leprosy yet found.

Historically, disfiguring diseases — particularly leprosy — caused the afflicted individuals to be ostracized from their communities. But apparently this sufferer, based on a number of things like the location and size of the tomb, the type of textiles used as shroud wrappings, and the clean state of the hair was a fairly affluent member of society in Jerusalem and that tuberculosis and leprosy weren’t confined to the poor in the first century AD.

The man was also wrapped in a burial shroud and this is the first time that fragments of shroud material have been positively dated to the first century AD. The shroud is very different to that of the Turin Shroud, hitherto assumed to be the one that was used to wrap the body of Jesus. Unlike the complex weave of the Turin Shroud, this is made up of a simple two-way weave.

Based on the assumption that this is a typical burial shroud widely used at the time of Jesus, the researchers conclude that the Turin Shroud did not originate from Jesus-era Jerusalem. The researchers also found a clump of the shrouded man’s hair, which had been ritually cut prior to his burial.

The first indication of the origins of an ancient and modern scourge and a simple burial shroud. History has much to teach us about ourselves.

This is a sample of the shroud which shows the simple two-way weave used for burial shrouds in 1st century C.E. Jerusalem. (Credit: Prof. Shimon Gibson)

Now we’ll travel forward in time again. We know what spears and burial shrouds can tell us, but what can we learn from books? Read on!

READ ALL ABOUT IT

Thousands of painstakingly handwritten books produced in medieval Europe still exist today, but scholars have long struggled with questions about when and where the majority of these works originated. Now a researcher from North Carolina State University is using modern advances in genetics to develop techniques that will shed light on the origins of these important cultural artifacts.

Many medieval manuscripts were written on parchment made from animal skin, and the researchers are working to perfect techniques for extracting and analyzing the DNA contained in these skins; Their long-term goal is to create a genetic database that can be used to determine when and where a manuscript was written.

The genetic testing will create a baseline using the DNA of parchment found in the relatively small number of manuscripts that can be reliably dated and their origin points fixed. Each manuscript can provide a wealth of genetic data because a typical medieval parchment book includes the skins of more than 100 animals.

Once the researchers have created a baseline of DNA markers with known dates and localities, they can take samples from manuscripts of unknown origin. Then they can determine the degree of relationship between the animals whose skins were used in manuscripts of unknown origin and those used in the baseline manuscripts. They hope this DNA comparison will enable them to identify genetic similarities that would indicate the general time and locale where a book was written.

It may also allow us to trace the trade route of parchments throughout the medieval world; a scholarly achievement that would provide a wealth of data on the evolution of the book industry during the Middle Ages.

A Greek Gospel from the 10th century. Researchers are using modern advances in genetics to develop techniques that will shed light on the origins of medieval manuscripts. (Credit: iStockphoto/Arpad Benedek)

A little march through time as we learn a little more about ourselves.

TB AND TEETH

By Pam Eastlick

Welcome to The Deep science and technology column where we cover topics from the deep sea to deep space and beyond.

Well, the medical bag is full to overflowing this week so we’ll learn some more tales of the things that affect the human animal. Our first stories deal with one of the planet’s deadliest killers: tuberculosis. We thought we’d all but wiped out this deadly scourge in the middle of the last century when we began to develop our arsenals of antibiotics. But it turns out that TB is not only a deadly enemy, it’s a wily one and our first story should chill you to the bone, given TB’s prevalence, not in some far-off never-never land, but right here in the Marianas.

DISEASE VS. DRUGS

We’ve known for a long time that TB is a shape-shifter when it comes to antibiotics. It seems that virtually every few months we read about yet another strain of TB that’s become resistant to yet another drug developed to combat it. But the latest update has a terrible twist.

Scientists have identified a strain of antibiotic-resistant TB that thrives in the presence of rifampin, a front-line drug used to treat it. The latest strain was identified in a patient in China.

The doctors researching this particular strain discovered that it wasn’t one of the fast growing types UNTIL you treated the patient with rifampin. Then, it took off like a rocket. They also observed that the patient’s condition grew worse when they were given rifampin, but they were cured with rifampin-free regimens.

Roughly 5% of all TB cases are resistant to isoniazid and rifampin, two of the main drugs used to treat the disease. And now we have a TB strain that is feeding on and dependant on the drug that was developed to kill it.

The researchers say that rifampin-dependent tuberculosis is difficult to detect and may be a bigger problem than we currently realize, since the resistant bacteria don’t grow well in culture mediums unless rifampin is added. The researchers urge public health workers to closely examine patients who aren’t getting better when given rifampin, to see if they harbor the rifampin-eating strain.

Unfortunately, the researchers note that drug susceptibility testing is time-consuming and not easily performed in resource-poor settings where tuberculosis is frequently more common.

The World Health Organization (WHO) estimates that tuberculosis kills approximately 2 million people worldwide each year. Multidrug-resistant tuberculosis (MDR-TB) is becoming an increasing problem in many parts of the world, largely because many patients take the antibiotics until they feel better and then they stop taking them. DON’T DO THAT!! That’s how you personally can create drug resistant disease!

And now in a bizarre twist, scientists have discovered that another bacterium that causes disease and kills many people may be an effective weapon against . . . wait for it . . . tuberculosis!

DISEASE VS. DISEASE

It’s been implicated as the bacterium that causes ulcers and the majority of stomach cancers, but studies by researchers at Stanford University, UC Davis, and the University of Pittsburgh have found that Helicobacter pylori (H. pylori) also may play a protective role — against (you guessed it!) tuberculosis.

Jay Solnick, UC Davis professor of medicine and microbiology, and his co-authors report that H. pylori infection may enhance immunity against tuberculosis, a disease endemic in many parts of the world, and for which there is no effective vaccine.

"Here is a bacterium that we know is sometimes harmful and that is clearly associated with cancer," Solnick said. "But it’s not that simple."

Solnick explains that up until the 20th century, when public health improved and antibiotic use was widespread, virtually everyone was infected with H. pylori. That remains the case today in most developing countries, implying that H. pylori may have evolved with its human host because it confers some selective benefit.

"These new findings suggest that one such benefit may that H. pylori provides protection against tuberculosis, and perhaps other infectious diseases as well," he said.

Tuberculosis is second only to HIV as a cause of death due to a single infectious agent; an estimated one third of the world population has latent TB infection. But only 30 percent of people exposed to TB ever become infected, and only 10 percent of those infected will develop active tuberculosis disease.

"One explanation may be the presence of chronic infection of the stomach with H. pylori," Solnick said. The findings also may eventually aid in managing TB, since H. pylori infection may help determine whether someone infected with TB gets a latent, asymptomatic infection or active disease.

Early studies funded by the National Institutes of Health showed that a patient infected with H. pylori had elevated immune responses to TB antigens. The researchers then checked patients from immigrant populations in Santa Clara County, then in households in Gambia and Pakistan, where TB is prevalent. During the two-year study, they found that people exposed to TB who then developed the active disease were less likely to be infected with H. pylori than those who were not infected with H. pylori.

The researchers decided to test their theory in non-human primates. They examined 41 monkeys who were exposed to TB. The results were striking. Of the 30 monkeys that tested positive for H. pylori, only 5 developed active TB, but 6 of 11 monkeys that were negative for H. pylori developed active disease.

The authors acknowledge their findings are preliminary and propose several follow-up studies. First, they want to test whether experimental infection of H. pylori will protect monkeys from TB, and whether it enhances the protective effect of immunization. If successful, they will test a recombinant H. pylori strain that expresses TB antigens for possible immunization against TB.

Electron micrograph of H. pylori. (Credit: Yutaka Tsutsumi, M.D. Professor Department of Pathology Fujita Health University School of Medicine / Courtesy of Wikipedia)

Hmmmm. I think what we have here is a classic case of fighting fire with fire!

And now we turn our attention to yet another bane of human existence, at least many of us look at it that way. And that’s the trip to the dentist. Some of us (and you know who you are!) deal with awful pain and unsightly smiles because of our fears. I urge you to visit the dentist if you have problems; particularly if it’s been years since you went. New techniques have definitely eliminated most of the ‘torture-chamber’ aspects of the dentist office. And the following articles tell us about the possible elimination of two more.

LOOK MA, NO MERCURY

Most of us acquired our fear of the dentist in childhood when the dentist made holes in our teeth and filled them up with black stuff. The holes the dentist made were to make holes we already had bigger.

Tooth enamel is the hardest material in the human body because it’s made almost entirely of minerals. As tough as it is, however, enamel can be broken down by bacteria. This forms holes that we all know as cavities and if you don’t go see the dentist regularly, the cavities will eventually destroy the tooth. That’s why dentists repair cavities by filling them with a material to replace the lost enamel. The most common such filling material was invented in the 19th-century and it’s called amalgam — the classic silver-black fillings many people have.

Amalgam works well because it is very durable, easy to use, and (most importantly) cheap. The dark fillings can be unsightly (as a child I had a lovely black hole between my two front teeth) but the real problem is that they contain mercury, a real health and environmental no-no.

Because of the mercury, amalgam has raised health and environmental questions — though according to the American Dental Association, the mercury is bonded in amalgam in such a way that it poses no health hazards.

Dentists would love to have a perfectly white material that mimics natural enamel for repairing cavities in teeth and doesn’t use mercury, but for the most part, they still use amalgam. Other filling materials have been developed, but they often have problems with shrinkage or durability.

Kent Coulter and his colleagues at Southwest Research Institute in San Antonio have developed a new dental restorative material under a program funded by the National Institutes of Health. The new fillings are made with a plastic-like material containing zirconia nanoplatelets — tiny crystals made of the same sort of material used to make fake diamonds and gem stones. Unlike their costume jewelry cousins, the zirconia nanoplatelets are super hard because of a difference in the particular arrangements of the atoms in the material.

Coulter and his colleagues designed a way to make a roll of this material under vacuum. They hope this material can be lifted from the roll and packed in a dental cavity and then cured — using an ultraviolet lamp or some other means — so that it hardens in place without shrinking. Zirconia nanoplatelets are still several years away from the dentist’s chair, however, and the next step will be to see if the new material performs as hoped for people with cavities.

Well, we hope that zirconia works in the mouth as well as it does on the finger, but for most of us dental sufferers, the problem isn’t the nasty black fillings, particularly if they’re inside the mouth and not front and center. The problem that keeps most people out of the dentist’s office is the DRILL. Read on, there may be hope there too!

A STAR IN YOUR MOUTH

One of the first misconceptions I tell my Astronomy students about is the ‘fact’ that the Sun is made from gas. Tell a first-grader this and they automatically assume the Sun is made from burning gasoline. As we get older, we figure out what a gas really is when we learn about the three states of matter, solid, liquid and gas.

Well, that one’s wrong too. There are actually FOUR states of matter and the most common one is the one you’ve never heard of. It’s plasma, the stuff stars are really made of. Plasma is ionized gas and it can have the characteristics of a solid and liquid and a gas.

Plasmas are common everywhere in the cosmos, and one of their characteristics is that they they’re highly reactive. For instance, scientists have discovered that high temperature plasmas react with oxygen and that makes them capable of destroying microbes. These hot plasmas are already used to disinfect surgical instruments.

We know how to make low temperature plasmas too, and it turns out that firing low temperature plasma beams at dentin — the fibrous tooth structure underneath the tooth’s enamel coating — was found to reduce the amount of dental bacteria by up to 10,000-fold. This means that plasma technology could be used to remove infected tissue in tooth cavities — a practice that conventionally involves drilling into the tooth.

Scientists in Germany have used these low temperature plasmas against common oral pathogens. These bacteria form films on teeth surfaces and are capable of eroding tooth enamel and the dentin below it to cause cavities. If left untreated it can lead to pain, tooth loss and sometimes severe gum infections. In this study, the researchers infected dentin from extracted human molars with four strains of bacteria and then exposed it to plasma jets for 6, 12 or 18 seconds. The longer the dentin was exposed to the plasma the greater the amount of bacteria that were eliminated.

These low temperature plasmas are right around body temperature which means that the dentist won’t have to fry your mouth to use them. The low temperature means the plasmas can kill the microbes while preserving the tooth.

The researchers say that plasma technology to disinfect tooth cavities would be welcomed by patients as well as dentists. As most of us know, drilling is usually uncomfortable and sometimes painful. Cold plasma, in contrast, is a completely contact-free method that is highly effective. The scientists are diligently working and they say that a clinical treatment for dental cavities can be expected within 3 to 5 years.

From TB to teeth. Science is an incredibly rich feast.

FROM LARGE TO SMALL

By Pam Eastlick

Welcome to The Deep science and technology column where we cover topics from the deep sea to deep space and beyond.

Well, this week I actually counted the items in each bulging file folder and discovered that the animals win hands down. Next biggest is what ails us humans, but we’re doing animal stories this week for sure and we’re starting with the biggest and moving on to some of the smallest.

LOVE SONGS OF THE BOWHEAD

Not so very long ago, the bowhead whale was written off as extinct in the waters around Disko Bay in northwestern Greenland, but the situation has changed and adult bowhead whales, which can be 50 feet long and weigh 100 tons, have returned to the bay. This is because global warming has opened the Northwest Passage, making it ice free in the summer. The bowhead whales from the northern Pacific are returning to Greenland and mating with the small local population for the first time in 125,000 years.

If this weren’t big enough news, Outi Tervo, a PhD student doing research at a field station on Disko Island has discovered some very interesting news about the lead-up to that mating.

Her research team placed hydrophones in Disko Bay and discovered that bowhead whales have developed very sophisticated songs to attract a mate. It turns out that bowhead whales sometimes sing with ‘more than one voice’. They produce two different songs or sounds and mix them together, and bowheads seem to be the only baleen whales that do this. Bowheads also change their songs from year to year and never repeat songs from previous years.

The bowhead whale is in the same weight class as fin whales and blue whales but they produce much more complicated songs, at higher frequencies, between 100 and 2000 hertz – cycles per second. And interestingly enough, the bowhead whale is the only species of ’singing’ whale where the gender of the singers can’t be detected from the song.

So, we have populations mixing that haven’t seen each other in 125,000 years. I suspect that REALLY gives them something to sing about! But that’s not our only whale song story. Read on!

SINGING THE BLUES

While the love song of the bowhead is being sung to new ears, the frequency of the songs sung by blue whales has been steadily creeping downward for the past few decades according to researchers at Scripps Institution of Oceanography at UC San Diego. They feel this lowering of pitch may be good news for the population of the endangered marine mammal.

The scientists studied blue whale song data from around the world and discovered a downward curve in the pitch, or frequency, of the songs. T he decline was tracked in blue whales across the globe, from off the Southern California coast to the Indian and Southern Oceans.

"The basic style of singing is the same, the tones are there, but the animal is shifting the frequency down over time. The more recent it is, the lower the frequency the animal is singing in, and we have found that in every song we have data for," said John Hildebrand, a professor of oceanography in the Marine Physical Laboratory at Scripps.

The researchers examined a list of possible causes for the frequency drop-from climate change to a rise in human-produced ocean noise-and believe it may be explained by the increase of blue whale numbers following bans on commercial whaling activities.

While the function of blue whale songs is not known and scientists have much more to learn, they do know that all singers have been determined to be males and that the high-intensity, or loud, and low-frequency songs propagate long distances across the ocean. Blue whales are widely dispersed during the breeding season and it is likely that songs function to advertise which species is singing and the location of the singing whale.

In the heyday of commercial whaling, as blue whale numbers plummeted, it may have been advantageous for males to sing higher frequency songs, the researchers believe, in order to maximize their transmission distance and their ability to locate potential mates (females) or competitors (other males). They think that when whale densities rise, the females are closer it’s easier for the song to reach her and easier for the whale!

When whales sing, they must use most of the air in their lungs. It’s harder to use the higher pitches and they use more air, just like the sustained notes produced by an opera singer. Blue whales sing to attract females, but if they have to use too much of their energy to sing, it’s harder to do things like eat.

The scientists say the same downward pitch phenomenon may be true in other whales such as fin and humpbacks, but the blue whale song, with a comparatively easier song to analyze, is a good springboard to study other species. The researchers say such knowledge about whale songs could be important in monitoring whale populations and recovery efforts.

Blue whale. (Credit: NOAA Fisheries)

Now we turn our attention from the largest of animals to some of the smallest. Consider the ant . . . . .

HOW DOES YOUR GARDEN GROW?

Well, Guam is drying out and that usually means that within a couple of weeks, I’ll be under siege. The ants have already started coming in the bathroom windows in search of water and then the kitchen will be next. Although they are only annoying for the most part, the fire ants get nuked with insecticide until they glow. Ants perform many valuable services; I just wish they wouldn’t choose my house in which to do them!

But there’s interesting news about another kind of ant that to my knowledge isn’t found here on Guam (although given our propinquity for invaders, it’s probably only a matter of time). It seems there are ants who are farmers.

Leaf-cutter ants, which cultivate fungus for food, have many remarkable qualities and here’s a new one to add to the list: the ant farmers, like their human counterparts, depend on nitrogen-fixing bacteria to make their gardens grow. The research highlights a previously unknown symbiosis between ants and bacteria and provides insight into how leaf-cutter ants have come to dominate the American tropics and subtropics. (Ah, explains why we don’t have them here!)

This partnership between ant and microbe allows leaf-cutter ants to be amazingly successful. Their underground nests, some the size of small houses, can harbor millions of inhabitants. In the Amazon forest they comprise four times more biomass than do all other land animals combined. (And I’m really happy we don’t have them here!)

The new study shows the nitrogen, which is extracted from the air by the bacteria, ends up in the ants themselves and, ultimately, benefits the nitrogen-poor ecosystems where the ants thrive.

The fungus-growing ants are technically herbivores. They make their living by carving up foliage and carrying it back to their nests in endless columns to provide the raw material for the fungus they grow as food. But the plants have less nitrogen than the ants need to survive.

Enter the nitrogen-fixing bacteria, two species of which were isolated in laboratory and field colonies of the ants. But merely finding the bacteria wasn’t enough. It was necessary to prove that the ants were actually utilizing the nutrient to confirm a true mutualism.

One other type of insect, the termite, has been previously shown to utilize nitrogen-fixing bacteria. And other bacteria-ant symbioses have been documented. However, the discovery of the nitrogen-fixing mutualism in ants has significant ecological implications, because ants are dominant in virtually all of the world’s terrestrial ecosystems. The new work suggests that an important source of nitrogen in the American tropics and subtropics is derived through the partnership of ant and bacteria.

So . . . . they’re farmers and they cultivate bacteria. But that’s not the only interesting story about leaf-cutter ants. They may have picked up cozying up with bacteria, but they’ve given up cozying up to something interesting. Read on!

These leafcutter ants are located on a spongy fungus garden, which they grow themselves.

WHERE HAVE ALL THE BOYS GONE?

Scientists have recently discovered that a species of fungus-gardening ant is the only ant species in the world known to have dispensed with males entirely.

Most social insects—the wasps, ants and bees—are relatively used to daily life without males. Their colonies are well run by swarms of sterile sisters lorded over by an egg-laying queen. But, eventually, all social insect species have the ability to produce a crop of males who go forth in the world to fertilize new queens and make new colonies.

But scientists have recently discovered that queens of the ant species Mycocepurus smithii reproduce without fertilization and males appear to be totally absent.

Animals that are completely asexual are relatively rare, which makes this is a very interesting ant. Asexual species don’t mix their genes through recombination, so you’d expect harmful mutations to accumulate over time and for the species to go extinct more quickly than others. They don’t generally persist for very long over evolutionary time.

Previous studies of the ants, which are found in Puerto Rico and Panama, have pointed toward the ants being completely asexual. One study in particular, showed that the ants reproduced in the lab without males, and that no amount of stress induced the production of males.

Scientists believed that specimens of male ants previously collected in Brazil in the 1960s could be males of this species, but the researchers analyzed those males and discovered that they belonged to another closely related (sexually reproducing) species of fungus-farming ant.

After reviewing the literature on previous studies of these ants, the researches have concluded that the species is very likely to be totally asexual across its entire range, from Northern Mexico through Central America to Brazil, including some Caribbean islands.

As for the age of the species, the scientists estimate the ants could have first evolved within the last one to two million years, a very young species given that the fungus-farming ants evolved 50 million years ago.

Mycocepurus smithii ants tending their fungus garden. These are the only known completely asexual ants in the world. (Credit: Photo courtesy of Alex Wild

So, we farm and we have no males. There’s an alternate lifestyle for you!