Monthly Archives: March 2010

Aquarium gravel and water

It wasn’t too many years ago that the home aquarist paid very little attention to the water in an aquarium. Perhaps some of that was due to the fact that most of the water used was collected from ponds or rainwater catch. Now most of us get our water from our water taps. The water has been processed to insure that it is safe for us to drink. Our safe drinking water is not necessarily the best water for fish. Chlorination is usually part of the water cleaning process. That and other chemicals added to our tap water can be stressful and even fatal to some fish.

Fish cannot survive in waters that are too acid or too alkaline. The acidity is measured on a scale that is known as the pH scale, shorthand for potentiometric hydrogen ion concentration. A pH scale starts with the strongest acids measuring pH 1, and ending with the strongest alkali as low as pH 14. In the wild, waters that harbor fish can a range from an acidic pH of 4 to a basic pH of 9. Most home aquaria should be kept near a neutral pH of 7 unless the specific species you have require something else.

There are ways to measure the pH of the water in an aquarium. The easiest is probably the litmus paper strip. To obtain a reading, dip the paper strip into the water and compare the color of the paper with a chart. This is a fast and easy method but can be inaccurate. The chemically treated paper can be affected by age and storage conditions.

A better and more accurate way to test the water is to obtain a kit that provides a vial and indicator chemicals. Water is collected in the vial and then the chemicals are added. The water changes color to indicate the pH.

Besides the source of the water there are other factors that can affect the pH and the degree of hardness of the water (DH). The aquarium ornaments we add to our tanks can slowly leach out calcium and magnesium salts. The ornaments include aquarium gravel, stones, or metals that are place in the water.

Prevention and cure of a pH or DH problem starts with using only aged water. That is water that has been collected and allowed to sit in a loosely covered pail for a day or two before adding it to the aquarium. Another preventative step is to buy aquarium gravel approved for aquarium use by being pH and DH tested. Rocks and stones should be of a non-metallic nature and free of limestone.

Before placing anything in an aquarium it should be washed and allowed to soak in clear water for a few days. The water should be tested before and after the soaking. If the pH or DH changes discard the object or try treating it with a mild solution of Hydrochloric acid then rinse thoroughly. Try the soaking and testing again. Your fish will thank you.

Essential advice for starting a home aquarium
Aquarium stands, options and considerations
Aquarium backgrounds

An introduction to travertine tiles

If you are considering a home improvement project that involves floors or tiles, consider using travertine tiles. Travertine is formed by the precipitation of carbonate minerals from ground, surface, or geothermally heated spring waters. This occurs where the water comes in close proximity with magma at some depth. While the water circulates and heats, it picks up dissolved minerals and solids. Those minerals are re-deposited when the water cools.

Typically, the crystallized minerals are calcium-based, or calcareous. The different impurities within the deposit contributes to the color and pattern of the stone. The random distribution of the colors gives each stone a unique design, which is one of the main appeals of this material.

In the United States, one of the best known areas where travertine is prevalent is in the Yellow Stone Basin in the National Park. There, geysors like Old Faithful circulate water in subterranian networks where it is heated. In the case of geysors, the water reaches a temperature where the steam pressure overcomes the overlaying water and it erupts in a dramatic display of steam and hot water. In other places, like Mammoth Hot Springs, the warm water comes to the surface less violently, but builds up deposits of travertine layer upon layer.

Mammoth Hot Springs at Yellowstone National Park where travertine is deposited from the geothermal waters.

Decorative stones are cut from source blocks in the quarry (not, of course, in the national park), and then taken for further processing. Based upon the intended use of the stones, they are cut and sized accordingly. Since the stone was originally deposited in a water environment there are usually many holes and pits. Frequently, these holes are filled with epoxy, cement, and dyes, but it can be used in its natural state if an uneven surface is no problem. The stone can also be honed or polished.

There are two or three small travertine quarries in the western United States. These quarries have a low production and the quality of stone is usually considered poor. A decade ago Italy had a near monopoly on the travertine market. Today Italy is still a leader, but has been joined by many other countries like Turkey, Mexico, and Peru.

Travertine has been used many ways. It can be used in a walkway, driveway, lanais, floor and wall covering, patio, and fountain. It can be used indoors and out. It has a wide variety of finishes and the price can be less than ceramic tile and wood flooring. When installed properly travertine will last the lifetime of a house.

Sore-mouthed dinosaurs

Benjamin Franklin quipped that the only thing in this world that is certain is death and taxes. He could have added disease to that list too.

There is a growing body of evidence that many of the diseases that humans and animals suffer from have followed us around from our earliest evolutionary roots. And recognizing disease in fossil animals can tell us a great deal about how the animals lived and give us insight into their everyday lives.

Take for example the well-known dinosaur specimen popularly called “Sue,” one of the most complete Tyrannosaur rex specimens known. Casts of its skeleton have been traveling to museums for many years in the exhibit “A T. rex named Sue,” amazing many people with its size and majesty. In the last weeks of Sue’s life she may have been a very cranky Dame indeed.

Upon viewing her skeleton, many have noticed the unusual holes along her left jaw. Those holes are not normal, but where they a sign of trauma, like wounds from combat? Turns out they are likely from a much small foe than another T. rex.

Left jaw of the dinosaur Sue showing pathologic holes

In a recent article (Wolff et al., 2009) researchers suspect that Sue, and other large carnivorous dinosaurs like her, were plagued by an infection of something like Trichomonas gallinae, a pear-shaped protozoan parasite that today infects birds. The parasite lives in the upper digestive tract of many bird species and causes sores in the mouth and throat. Some of the sores in modern birds have caused bone erosion that looks just like that seen in Sue.

Modern birds transmit the disease through discharge of body fluids. (This parasite does not attack humans). Adult birds that feed offspring can infect them directly for example. Infection is very common in modern birds, and infected birds may have no ill effects. It is not unlikely that in 65 million years of coevolution modern birds have built up resistance to the disease that their ancient cousins, the meat-eating dinosaurs, did not have.

It appears that Sue, and others like her, died of simple starvation, not being able to eat because of mouth and throat sores. An ignoble end perhaps, but showing that this thing we call life can change on the smallest circumstances.

WOLFF, E. D. S., S. W. SALISBURY, J. R. HORNER, AND D. J. VARRICCHIO. 2009. Common Avian Infection Plagued the Tyrant Dinosaurs. Plos One, 4(9):e7288.

Other dinosaur facts can be found here at Boneblogger. Search or select the category for more.

Experiences in setting up a home aquarium

My aquarium experiences started off as something of an accident. My partner and I were given a 5-gallon fish tank with a simple over the side fiberglass filter. The tank also included a few guppies and mollies.

We set up the tank on a small aquarium stand near our eating area. It turned out that the tank became our mealtime TV. We could watch the fish swim and eat while we ate our evening meal. The slow movement through the water was accented by the mating chase and the territorial disputes. It was exciting the first time we saw a baby fish being born. It was just as moving to see that same baby fish become fish food.

Knowing very little about having an aquarium we also knew very little about how to best keep our newborn fish alive. One store suggested we use a breeding cage. The idea of the breeding cage is to place the mother inside a mesh cage or trap that would permit her to give birth. The babies would fall through the cage openings and the mother would not consume them. As you can easily imagine, this only protected the fry from the birthing mother and not from the other fish. In order for that method to be effective it would require that each mother have a tank of her own until she was finished giving birth. That did not sound like a workable idea for us.

Similar to the cage is a breeding plate. This is a mesh plate that is inserted into a tank slightly above the aquarium gravel. The idea is that the fry can fall below the plate and have a protected area to start their life. We did not like the appearance of the plate and it made cleaning the gravel impossible. For a breeder who wanted to collect young fish and didn’t care how the tank looked this might be a good method of separating newborns from adults.

Another suggestion was to have lots of plants for the fry to be dropped in or near. They could then hide and avoid being eaten by all the bigger fish. This idea at least was workable. In our ignorance we planted the whole bottom of the aquarium in plants. The plants were not properly anchored down and soon we had one of the biggest floating gardens I have ever seen. All we could see was the floating garden, no fish. With a little practice, observation and a bit of advice from knowledgeable shop owners we learned the proper balance of plants to fish and other aquarium ornaments.

Essential advice for starting a home aquarium
Aquarium gravel and water
Aquarium Stands, Options and Considerations
Aquarium backgrounds explored

Musk ox say no to hunting

As we face the uncertain effects of climate change ourselves in the future it is instructive to look back in time to see how other species fared. (See also a geologic perspective on the effects of climate change.) Paleontology is one of the main sciences involved in this research and so proves to be very relevant to this modern issue.

A recurring mystery in paleontology is the cause of the most recent major extinction event at the end of the Pleistocene or Ice Age. Many large species of mammals, collectively referred to as megafauna, became extinct relatively recently, a mere 10,000 years ago more or less. Charismatic animals such as mammoths, mastodons, giant ground sloths, and saber toothed cats vanished from the Earth forever.

It has long been debated what the primary cause of this extinction event was. Just as with other major extinctions observed in the fossil record, there are a number of suspected causes for Ice Age extinctions: disease, climate changes, and extra-terrestrial phenomena like asteroids. But the Ice Age extinctions have another factor that previous extinction events do not have—the emergence of humans as a major player upon the landscape. Did human activities, maybe the over hunting of the megafauna, drive them to extinction?

Many studies have tried to get at this question, but it is very difficult to separate all the confounding issues from each other to focus on just one to test its potential effects. A new study however was able to do just this.

In a recent paper (Campos et al., 2010) DNA material was extracted and analyzed from one of the species that did survive the Ice Age extinctions, the musk oxen. This Ice Age relic lives today mainly in the high-latitudes of Greenland and Canada, but was once more wide-spread. Indeed, its remains have even found as far south as Nebraska, New York, and Ohio during the Pleistocene.

Musk oxen are well adapted to the extremes of arctic living with sturdy bodies and thick coats of hair.

The researchers collected samples from across the musk oxen’s former range for the last 60,000 years. They examined the DNA to look for patterns of population dynamics over that period. Basically, when a population is strong and has many members the DNA samples show an increase in diversity—more genetic variation in the mix. When populations suffer and numbers decrease the results show up in the DNA as a decrease in diversity, sometimes referred to as a genetic bottleneck. So, the DNA diversity over time shows a proxy for population numbers and health.

Therefore, if humans were a prime driver of population declines for musk oxen at the end of the Ice Age we would expect to see genetic bottlenecks within the DNA corresponding to the timing of human activity within the musk oxen’s range.

The DNA results show that the geographic origin of all the musk oxen DNA is northeast Siberia with a large diverse population. However, the population in that region crashed about 45,000 years ago. After that population decline, there was a world-wide genetic diversity increase about 30,000 years, followed by another decline about 18,000 years ago, and finally a slight recovery about 5,000 years to the modern relict populations.

With these data we can directly test for the first time the correlation of population declines of the musk ox with human activity. And, in fact, they do not correlate very well, suggesting that humans played little role in the population dynamics of musk oxen.

So, if not humans, what then was driving the populations to decline? The most likely cause was environmental changes, particularly climate changes. The Pleistocene is characterized by shifts in climate patterns with the best-known effect being glacial advance and retreat over the last 2 million years. It seems, at least in the case of musk oxen populations, that the pattern of boom and bust was driven by their ability to adapt to climatic changes in their environment. Musk oxen almost went the way of the mammoths and succumbed fully to extinction, but managed to just hold on by their horns in greatly reduced numbers until today.

Of course, whether they, or any other species that are similarly at risk, will weather the next several decades, and any modern climate changes, remains to be seen. The effects of climate change may well prove to be too much for them after all.

CAMPOS, P. F., E. WILLERSLEV, A. SHER, L. ORLANDO, E. AXELSSON, A. TIKHONOV, K. AARIS-SØRENSEN, A. D. GREENWOOD, R.-D. KAHLKE, P. KOSINTSEV, T. KRAKHMALNAYA, T. KUZNETSOVA, P. LEMEY, R. MACPHEE, C. A. NORRIS, K. SHEPHERD, M. A. SUCHARD, G. D. ZAZULA, B. SHAPIRO, AND M. T. P. GILBERT. 2010. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceeding of the National Academy of Sciences.

Boneblogger: Science and the outdoors

Exploring the natural world