Coral Can Call for Help

This broad-barred goby is one of the species that responds to a coral's call for help (click for credit)

Anyone who has read this blog for a while knows that I am fascinated by the mutualism that seems to be all over creation. You can seem some of my previous posts about this topic here, here, here, here, and here. I recently came across a study that provides another example of mutualism in one of favorite habitats: a coral reef. As an amateur scuba diver, I spend a lot of time enjoying the wonders of coral reefs, and the more we study their biology, the more amazed I am at the interconnectedness that exists among their inhabitants.

The authors of the study were trying to understand how a very common species of coral, Acropora nasuta, protects itself against the toxic seaweed Chlorodesmis fastigiata. This particular seaweed attempts to take over a coral reef by producing chemicals that harm the coral. The chemicals reduce the coral’s ability to grow and feed, allowing the seaweed to “muscle in” on the coral’s turf. When the seaweed is completely successful, it chokes out the coral, forming a shrubby thicket where the coral once was.

As the authors note, previous studies have already shown that overfished coral reefs are more likely to be taken over by such seaweed, so they wondered if perhaps the fish that live in the coral reefs provide some sort of protection for the coral. They found that certain species of goby (particularly the broad-barred goby, Gobiodon histrio, and the redhead goby, Paragobiodon echinocephalus) do, indeed, protect the coral from the seaweed, but the process by which this happens is rather surprising.

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Homing Pigeons May Hear Their Way Home

These homing pigeons can usually find their way home over very long distances. (Click for credit)
Homing pigeons have been bred to be able to find their way home, almost no matter where they are released. They have been used for more than 2,500 years to deliver messages in a fast, reliable way. For example, a homing pigeon was used to deliver the results of the first Olympiad back in 776 BC.1 Because they have been used for such a long time, scientists have tried to figure out how pigeons are able to navigate their way from an unknown location back to their home. While scientists have been able to figure out some aspects of homing pigeon navigation, the details haven’t been entirely worked out.

It was once thought that homing pigeons use visual landmarks to help in their navigation, but experiments in which the pigeons’ eyesight was reduced using frosted contact lenses showed that’s not correct. Other experiments demonstrate that homing pigeons can sense the earth’s magnetic field, but many of those same experiments also show that disrupting that sense doesn’t always end up leading the pigeons astray. In addition, some experiments indicate that homing pigeons use the position of the sun in the sky to orient themselves, but that can’t be the entire explanation, either, because pigeons can navigate even on very cloudy days. It seems, then, that pigeons use a wide variety of strategies to navigate their way home.2

The mystery of homing pigeon navigation deepened back in 1997, when the Royal Pigeon Racing Association decided to celebrate its 100th year anniversary by releasing 60,000 pigeons in the south of France. These pigeons came from homes throughout southern England, and they were expected to be able to reach those homes in a few hours. While a few thousand of them ended up returning to their homes over a period of a few days, most never made it back.3

Over the years, several hypotheses have been put forth to explain why those pigeons never made it home. One of them suggests that the pigeons’ navigation was disrupted by the sonic boom of the Concorde jet whose flight path crossed that of pigeons. A recent study by Dr. Jonathan T. Hagstrum adds some support to this hypothesis.

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Nature’s Farmers Are Pretty Smart!

The Central American agouti collects seeds and buries them for later use. (Click for credit)

When I was in Costa Rica last year, I saw several Central American agoutis, such as the one pictured above. I didn’t know anything about them, so when I got back home, I looked up some information. They can be omnivorous, but they prefer to eat seeds and fruit. One of their interesting behaviors is to follow troops of monkeys. They “hang out” underneath the trees that the monkeys climb, and they eat the fruit that the monkeys drop or inadvertently shake off the trees.1

Another really interesting thing about the Central American agouti is that it’s a scatter hoarder.2 This means it collects seeds and buries them in multiple locations. It remembers these locations and returns to them when food is scarce. However, it doesn’t just bury them once and leave them there. It often revisits its stores of seeds, digs them up, and reburies them somewhere else.

While this behavior is beneficial to the agouti (it provides storehouses of food for when food is scarce), it is also beneficial to the trees that drop the seeds. That’s because the agouti rarely uses all of its stored seeds. As a result, some of the buried seeds grow and develop into new trees. This means that the Central American agouti is, in fact, a “farmer” for the trees. It moves seeds away form the tree that drops them and plants the seeds so they can grow into new trees.

Why is this beneficial to the trees? If a seedling grows too near the tree that dropped the seed, it ends up competing with its parent tree. That’s not good for the parent or the seedling. By carrying the seed far from the tree and planting it, the agouti allows the seedling the chance to grow without competing with its parent. Pretty nifty, huh? Well, recent research shows its even niftier than that. It turns out that these “tree farmers” are smarter than we originally thought.

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Why (and How) Your Skin Wrinkles Underwater

When immersed in water for a long time, the skin on your hands and feet wrinkles.
(Photo by Brenderous, click for full credit)

Almost everyone has experienced it. When you have been soaking in the bathtub, swimming, or just washing dishes for a long time, the skin on your fingers (and toes) wrinkles. From a scientific point of view, there are at least two questions to consider: (1) How does this happen? and (2) Why does this happen? Most textbooks explain (often incorrectly) the how, but I haven’t found any that explain the why. It seems that over the years, scientists have been studying this, and in the end, they have mostly answered both questions.

Let’s start with the “how.” A lot of textbooks and websites incorrectly explain this part. They say that it is the result of your skin absorbing water and swelling. It turns out that’s not true at all. More than 70 years ago, scientists showed that if certain nerves to the hand are damaged, its skin will not wrinkle, no matter how long it stays underwater.1 Over the years, other scientists have investigated water-induced wrinkling, and it seems to be the result of a process initiated by the nervous system.

Your skin is made of two layers: the epidermis (the layer you see) and the dermis (the layer underneath that contains blood vessels). When your hands and/or feet have been underwater for a long time, your nervous system tells the blood vessels in your dermis to constrict. This reduces the volume of the dermis, which in turn reduces the tension with which the epidermis is stretched. As a result, the epidermis “relaxes,” forming wrinkles.2

This answer is interesting enough, because I have long taught the incorrect explanation for how your skin wrinkles underwater. I am glad that I learned I was wrong on the point, and I will now start teaching the correct explanation. However, the “why” question is also very interesting, and a couple of recent studies have provided a good answer for that question as well.

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Even Shark Embryos Detect Electric Fields

A bamboo shark embryo in its egg case (Image from the study being discussed)

I have always been fascinated by sharks. In fact, of all the times I have been scuba diving, the dive I remember the most occurred off the coast of South Africa. I went with some marine biologists who had been studying sand tiger sharks (Carcharias taurus). As I initially sunk down into the water, I leveled out just a few feet from the bottom, and as I was checking my gauge to determine my depth, a 2-meter (6-feet) long shark swum right underneath me! We ended up seeing more than a dozen sharks of various sizes on that dive. It was incredible.

One of the things that is fascinating about sharks is the way they hunt. While they use their sense of smell (and to some degree their sense of sight), one of their main hunting techniques involves using their electrical sense. Yes, sharks can sense electrical fields, and they are quite good at it. As a recently published book on sharks says:1

They can detect the minute electrical currents generated by the nervous systems of prey by using electrical sensors called the ampullae of Lorenzini…These sophisticated sensors are very useful in finding prey buried under the sand.

Interestingly enough, these sophisticated sensors often develop while the shark is still an embryo. Is that just to get the shark ready for hunting its prey when it is fully developed, or could there be some use that the embryo has for sensing electrical fields? It doesn’t need to hunt, so for what purpose could it be using its electrical sensors?

Some Australian scientists decided to investigate this issue, and what they found is fascinating!

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Sockeye Salmon Use Geomagnetic Details to Guide Them Home

A sockeye salmon jumps a beaver dam to get back to the stream from which it hatched. (Click for credit)
Salmon have an incredible lifecycle. They hatch in freshwater streams, eat and mature a bit, and then they make their way into the ocean. They do most of their growing and maturing in the ocean, and when they are ready to reproduce, they return to the very stream from which they hatched to find a mate and begin the cycle all over again.

A lot of research has been done trying to figure out how the salmon know the way back to the specific stream from which they hatched. Well, each stream has it own mix of soil, rocks, and other environmental elements. As a result, each stream has its own specific mix of chemicals. Most of the data indicate that a salmon remembers the specific chemical makeup of its original stream. Once it gets back to freshwater, then, it starts following a “chemical trail” that will lead it back to the stream from which it hatched.1

While this is rather impressive, it doesn’t really tell us about the most difficult navigational aspect of the journey. The salmon spends a long time in the ocean growing and maturing. As a result, it often ranges far from the place where it entered the ocean. How does it find its way back to the correct freshwater inlet that will lead to the correct stream? It seems hard to believe that it could follow a “chemical trail” that far! Since we know that salmon are equipped with biological machinery that allows them to sense the earth’s magnetic field, it has been thought for some time that salmon use magnetic guidance to get them to the proper freshwater inlet.2

While that’s a reasonable conclusion based on what we know, there hasn’t been a lot of evidence to back it up. However, a recent study published in Current Biology has begun to remedy that situation.

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Hippopotamus “Sweat”

This circus poster promoted the myth that hippos sweat blood. (Public domain image)
I am currently in Thailand, speaking at a family education conference. There are a lot of incredibly wonderful families here, and not surprisingly, some of them feel a bit overwhelmed at homeschooling their children in Asia. To all those homeschoolers in the United States: be thankful for all the support that exists where you live. Home education is difficult enough when there are support groups, easy access to curriculum, and homeschooling conferences that showcase multiple speakers and vendors. Imagine trying to homeschool with without such luxuries. That’s what these families do every day.

Because I am one of the few speakers at this conference, I have been giving a lot of talks. However, my favorite thing to do is answer questions. As a result, one of my scheduled times with the parents was simply a question/answer session. It went really well, and I hope I helped these parents with their unique situations. I was also scheduled for two sessions with the teens, and I made one of them a question/answer session as well.

When you offer a one-hour time slot for questions and answers, there is always a risk. What if the attendees have no questions? What if they have a couple of questions, but not nearly enough to last for an hour? I honestly didn’t think this would be an issue for the parents, since they face so many challenges homeschooling where they are. However, I did worry about the teens. While I was sure they had lots of questions, I was afraid they wouldn’t be “brave” enough to ask them in a group setting. To reduce the risk, then, I offered free candy for every question. Not surprisingly, the teens ended up having plenty of questions.

One of the reasons I love answering questions is that I often learn something new in the process, and this conference was no exception. The second question I got from the teens was:

What is the color of hippo sweat?

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Even More Impressive DNA Storage

DNA can store incredible amounts of information (montage of public domain images)
A few months ago, I wrote an article about a group of scientists who stored a book that contained words, illustrations, and Java script on DNA. It was an amazing technical achievement, and it demonstrated the incredible storage capabilities of this marvelous biomolecule. Well, another team of scientists has gone even further: they stored words, pictures, and audio on DNA!

Yes, the team encoded all 154 of Shakespeare’s sonnets, a photograph of the European Bioinformatics Institute (where the scientists work), and a 26-second audio clip from Martin Luther King’s famous “I have a dream” speech.1 Also, in a very fitting symbolic gesture, they added the famous James Watson and Francis Crick paper that first revealed the structure of DNA.2

This new achievement was noteworthy for more than just the fact that the scientists stored audio on DNA. While the method that the previous team used to store the book worked well, it was difficult for instruments to retrieve the information from the DNA once it was stored there. Thus, the time it took to retrieve the book from DNA storage was fairly long. The scientists who produced this study used a different method to store the information, which made it much easier for instruments to read it back. As a result, not only was everything retrieved from DNA storage with 100% accuracy, the time it took to get it back was significantly reduced.

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Being Degenerate Can Be Very Good!

DNA uses four nucleotide bases taken three at a time to code for an animo acid (click for credit).
The genetic code is degenerate, but that doesn’t mean it is immoral or corrupt. In fact, in the case of the genetic code, degeneracy is a good thing! Let me explain. One of DNA’s jobs is to tell the cell what proteins to make and how to make them. As a result, it stores “recipes” for proteins, and we call those recipes genes. Well, a protein is produced when smaller chemicals, called amino acids, are linked together in long chains that then fold into intricate shapes. So in order to tell a cell how to make a protein, a gene needs to list a string of amino acids. If the cell puts those amino acids together in the order specified by the gene, the correct protein can then be produced.

How does a gene list the amino acids? As shown in the illustration above, it does so by using the four nucleotide bases known as cytosine (C), guanine (G), thymine (T), and adenine (A). A group of three nucleotide bases codes for a specific amino acid. For example, when a gene has three thymines in a row (TTT), this means “use the amino acid called lysine.” When it has three guanines in a row (GGG), it means “use the amino acid called proline.” So by grouping its four nucleotide bases three at a time, a gene specifies which amino acid should be used in building a protein.

Here’s the catch: There are only 20 amino acids in the standard proteins of life. As a result, there need to be only 20 codes to specify them. However, there are 64 possible ways you can group four nucleotide bases three at a time. Thus, there are 64 different possibilities for how a gene can specify an amino acid, but there are only 20 amino acids the gene needs to specify. As a result, most amino acids are specified by more than one set of three nucleotide bases. As I said above, a sequence of three thymines (TTT) means “use the amino acid called lysine.” However, two thymines followed by a cytosine (TTC) means the same thing. This is why we say the genetic code is degenerate. It has multiple ways it can specify most amino acids.

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Poop Transplants Treat Clostridium difficile Infections!

Clostridium difficile from a stool sample, magnified 3,006x (public domain image fron the CDC)

Clostridium difficile is a bacterium that produces toxins which can kill intestinal cells and cause severe inflammation of the intestinal walls. Mild infections from this bacterium can cause diarrhea, while severe infections can cause death. Over time, C. difficile infections have gotten worse. As one medical resource states:1

C. difficile infection has transformed from a nuisance into a potentially life-threatening illness with an attributable mortality rate of up to 16.7%.

The typical treatment for severe cases of C. difficile infection is a round of strong antibiotics, but that doesn’t always work. A significant number of patients end up experiencing one or more recurring infections within 60 days.2 As a result, medical researchers are trying to come up with new ways to treat this infection.

In a recent study published in the New England Journal of Medicine, researchers tested an…interesting…approach. They took 43 patients who had a C. difficile infection and split them into three groups. The first received the standard antibiotic treatment (in this case, 500 milligrams of vancomycin four times per day for 14 days). The second received the standard antibiotic treatment plus a bowl lavage 4 or 5 days into the treatment. In case you aren’t familiar with the term, a bowel lavage involves flushing out the intestines. It is usually done to prepare the intestine for medical imaging. The third group was given a shortened round of antibiotics (500 milligrams of vancomycin four times per day for 4 or 5 days), a bowel lavage, and then a poop transplant.

Yes, you read that right. After the bowel lavage, the patients were given a mixture of water, salt, and the feces from a healthy donor. Now don’t worry. They didn’t have to eat or even smell the stuff. It was sent into their intestine through a sterile tube that went up the nose, down the esophagus, through the stomach, and into the start of the small intestine. While the process sounds incredibly gross, the results were amazing!

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