Category Archives: Science

Mammoth protein designed to be cool

Researchers were recently able to isolate and study woolly mammoth hemoglobin and compare it to the modern African and Asian elephants. They isolated the genes from DNA that code for the creation of hemoglobin, the protein that carries oxygen in our blood. This was done for both the modern elephant species, as well as from DNA from mammoth bone from Siberia. They observed some minor differences between all the species, so the researchers wondered if the difference in the mammoth’s blood might have helped it survive in cold climates.

Hemoglobin supplies our body with oxygen by carrying it around in our blood stream and then releasing it to our tissues. When our tissues need more oxygen, like for muscles that are working hard, hemoglobin more easily releases oxygen because of the higher temperatures created by the heat generated by the muscle. However, in colder temperatures, hemoglobin does not give up oxygen as easily. This is potentially a real problem in colder climates. To keep the hemoglobin to working effectively an animal might need to expend valuable energy to maintain a higher body temperature.

The researchers (Campbell et al. 2010) wondered if the slight differences in woolly mammoth hemoglobin might have been an adaptation for living in colder temperatures. They inserted the Asian elephant genes that make hemoglobin into the common bacteria, Escherichia coli, and allowed the bacteria to act on the genes, thereby making Asian elephant hemoglobin. This process is not new as it is commonly used to have bacteria produce proteins that are identical to human-made proteins, like insulin.

To get the bacteria to make mammoth hemoglobin, they needed to modify the Asian elephant genes the same way they observed, then let the bacteria make the hemoglobin of a mammoth—thousands of years after the mammoths last did it themselves. Researchers could then compare the protein of the two species directly. The result was that mammoth hemoglobin released oxygen much more effectively at lower temperatures.

Woolly mammoths from Alan Turner (2004), National Geographic Prehistoric Mammals.

Woolly mammoths were adapted to colder climates in a number of ways, such as compact bodies, small ears, short tails, and long woolly hair. This result strongly suggests that their bodies were also changed at the molecular level for life in cold, high latitude climates during the Ice Age. It would be very interesting to see if other mammoth species, such as the Columbian mammoth, for example, shared this adaptation. But I suppose that will have to wait until we can get good DNA from that species. All in good time.

Campbell, K. L. et al. 2010. Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics 42:536-540.

I am a paleontologist

I love the science of paleontology for many reasons. The science combines so many other areas of study into one bundle, such as geology, biology, functional morphology, evolution, stratigraphy, and systematics.

Not only that, dinosaurs and other prehistoric animals are just fun! And being fun, paleontology is a great way to introduce people to science in an engaging way. How many young people start their interest in science by learning about dinosaurs, and say they want to be a paleontologist when they grow up–a bunch!

Well, someone shared this video with me and I love sharing it with you. Enjoy! (you may need to scroll down).

Why dinosaurs are not extinct

In the twenty plus years I have been involved in paleontology I have been witness to a revolution within science. The revolution has been quiet, not noticed by most of the public. Like any good revolution, the battles of this revolution took place between two camps, the “traditionalists” and the “radicals” who were out to change things. And this shift is illustrative of how science as a whole moves from one way of understanding to a brand new way of looking at the world. It is, in fact, a paradigm shift that has profoundly changed biology and paleontology forever.

At issue is how we explore and classify the relationships of all living things. The traditional view, the one that I was taught as a young student, was the classification of living things into the taxonomy originally begun by Carl Linnaeus. This system started with a group, and then sought to put things into the group. For example, one can make the observation that animals that look like “dogs” could be grouped together, so you would start with the idea of a dog-group and look for animals that should be included.

You might put foxes, wolves, domestic dogs into the group, and call it the dog family. You might also note that “cats” could likewise be grouped, and do the same thing, creating a cat family. In this view, the families were equal in rank—and there could be no overlap. An animal would be included in only one of the equal-ranked families. Any animal was included in only one class, for example Amphibia, Reptilia, Aves, or Mammalia.

The equal-ranked heirarchy of classifications worked well enough when we mainly were concerned with modern animals. Clearly, birds look different than mammals and reptiles, so it seemed evident they belonged in their own class. But this classification scheme, however well it served us as a place to start, is myopic about how evolution actually operates—how organisms actually evolve. This is understandable since it was started 100 years before evolution as a theory was established.

In trying to shoehorn life into the system, we repeatedly ran into problems as we expanded our knowledge of the diversity of living things and our understanding that the history of life is a complex branching bush. We knew that early tetrapods (organisms with four limbs) gave rise to the early amphibians that crawled out on land, and that they in turn evolved into reptiles, mammals and birds. But despite this branching within tetrapods, the class ranks were forced to be exclusive, so somewhere in evolutionary history was an “amphibian” that had to become a “reptile,” and a “reptile” that had to become a “bird.”

The many transitional forms in the fossil record increasing became impossible to classify. These intermediate animals had to be forced into one class or another. Increasingly, it became evident that many times the criteria used to put an organism into one class were the whims of an individual scientist, and another equally qualified expert with different opinions might place the same animal in a different class with equal validity.

The origin of birds was for a long time a great mystery to paleontologists. Birds are a pretty unique and specialized group, and while we knew that they originated from reptiles somehow, exactly how and when was unclear. One early paleontologist noted that dinosaurs had many features in common with birds, but the early concepts of what dinosaurs were like distracted most scientists from comparing them too closely. After all, the common conception of dinosaurs was as big, lumbering, dim-witted, swamp-dwelling beasts. The bird ancestor must have been light, fast moving, and energetic.

However, dinosaur research over the last thirty years has completely changed our view of them. Evidence from many lines, including things like footprints and the cellular structure of the bones, all point to dinosaurs as being very dynamic creatures. With this new view, the notion that birds were linked to dinosaurs became clear too. Now, we have dinosaur fossils with feathers, and birds with teeth and dinosaur tails to attest to their close relationships. In fact, birds are most closely related to the meat-eating raptor-like dinosaurs of Jurassic Park fame.

To go along with the revolution in our view of dinosaurs was that revolution in science that I mentioned above–the emergence of a new way to understand the interrelationships of life on Earth. This new model accommodated the myriad branching events that life actually experienced in order to produce the great variety of living things. So, instead of starting with a conception of the group and looking for members, this new concept looked at the branching patterns evident in life, and then sought to apply names.

Below is an illustration of the branching pattern of selected tetrapods, those vertebrates with four well developed limbs. As the first tetrapods gave rise to new and different groups, the branches split off. An early tetrapod gave rise to amphibians and the other animals above it on the chart (mammals, turtles, etc.). A later tetrapod developed traits related to the production of eggs and young that we recognize as the Amniota. Some of those early amniotes went off on an evolutionary trajectory that we can recognize as being the early mammals, and all the diversity that resulted from them. And so it goes up along the branches.

Branching pattern of the tetrapods, mostly the land vertebrates

We now explore the branches and can apply names to the groups that we find to be meaningful. For example, in the illustration below we can call everything in the box a reptile. Note that it includes things that used to be called reptiles, turtles, lizards, snakes, crocodiles, and dinosaurs, but now also includes birds.

Group that includes all the reptiles

Likewise, if we draw a line around the dinosaurs, they also include the birds. This view of life tells a more complete evolutionary history and retains the branches, letting the animals “fall where they will.” We do not pull birds out of their relationships and give them special consideration. Instead of birds being equal in rank with reptiles, they are included among them. This upsets the tradition that being a bird is somehow equally important to being a reptile, but better reflects the reality of descent, without forcing nature into earlier human conventions of naming and grouping. Of course, birds are a group within their own right, and we could zoom in to explore their branching pattern, but it does not change the group to which they belong.

Group of dinosaurs

This leads to another startling statement. Below I have highlighted the groups that are extant (still around today).

Groups of tetrapods that are alive today (extant)

Because of our grouping scheme, birds are included in the dinosaur group, so dinosaurs are not really extinct! They live among us today flitting about, singing their mating songs in the trees. It is funny how things can change in science. Twenty years ago scientists would have told you the dinosaurs were all extinct, and today we say the opposite. I love scientific progress–it can be so startling.

3D Scanners In Archaeology

3d scanners are relatively new technology. Only the advent of the laser and computers has allowed for the transfer of all details about an object into a computer, and possibly the manipulation of these items with computer aided drawing (CAD) software or similar software. 3d scanners have a huge variety of uses, but perhaps the best use is for reverse engineering and cultural purposes.

Such devices have been used by archaeologists since the invention of the technology. This application is excellent for the purpose of finding hidden details in an artifact or piece of artwork that are too small for the eye to detect it. Also, as the technology typically uses lasers or sound waves for the purposes of scanning the object, it is minimally invasive. For example, a scientist or historian may want to know more about the content of an oil painting and the chemical properties of the paint. He or she could take a small chip of paint out of the painting, but if the painting is historic enough, that likely would not be allowed. However, oil paint is very well known for accumulating in large bumps, with a lot of texture. A 3d scan of the painting could likely give enough information about the structure of the painting to figure out the contents of the paint.

There are a number of famous examples of the use of 3d scanners in archaeology. Perhaps the earliest is two different groups of researchers who were able to scan Michelangelo’s famous statue David in 1999. Both of these groups used scans at a resolution of .25 mm, which accumulated a huge amount of data, detailed enough to see the chisel marks. These data were able to tell the researchers a large amount about how the statue was made, what tools Michelangelo had to work with, and other important archaeological information. Today, most famous works of art have been subject to the same treatment. And best of all, it is completely noninvasive.

Venom, Poison, and Toxicity

There is a great deal of confusion about the terms venom, poison, and toxicity, and they are often used in an imprecise manner. However, the subject is great fun, so let’s explore it a bit.

First, we should clear up the difference between venom and poison. Venom is a substance that is generally injected, such as through a bite. Poison is something that is ingested, such as by eating or inhaling. So, these words relate to how the substance is gotten from point A to point B. Therefore, it is not correct to describe a snake as poisonous, unless it caused you some reaction if you ate it (beyond the thought of eating a snake, that is).

Dance Macabre

Monarch Butterflies, on the other hand, are poisonous. They take up toxic substances from the food source of the caterpillars, the milkweed plants, and by concentrating the toxins in their body, they become poisonous to consume. This is a defensive mechanism, not so much for the individual, but for the species as a whole. Any single individual might get eaten, but the effect on the eater is hoped to be so unpleasant as to cause it to not want to eat another one, so the entire species benefits.

Toxicity refers more to the effects of poison or venom. It is a descriptive term used to characterize the medical impact. So, venom can be more or less toxic and still be venom. All spiders are venomous (that is, they inject a venom), but not all spiders are equally toxic, and therefore dangerous, to people.

And, not to put too fine an edge on it, there are things that are toxic without being venom or poison. If you save up a bunch of your saliva, and then loaded it into a syringe and injected it into your skin, you would find that it has a toxic effect on the injection site. That is, the proteins in the saliva would begin to act upon the proteins in your tissues, but we hardly consider humans venomous.

Venom is found throughout the animal kingdom and serves a wide variety of purposes. Some of the most dangerous animals are venomous. Venom can help secure food, as in wasps that sting their victims to lay eggs upon for feeding the larva, or in shrews that bite their prey and inject venom to help immobilize it. Spiders, too, inject venom, which helps immobilize and kill they prey, but it also begins the digestive process so the spider can feed upon the liquefied remains.

Venom can be defensive. For example, a colony of honey bees does not need venom to feed, but uses it as a deterrent to would-be intruders on the hive. Fish, such as the lionfish, have spines with venom that can be injected into attackers upon being bitten. And the male duckbilled platypus has a spin on its hind legs that can inject venom, used again rival males in courtship combat.

Snakes are some of the best known, and most misunderstood, of the venomous animals, and snake venom is diverse in its function and toxicity. In general, snake venom falls into two broad categories: hemotoxic and neurotoxic, but in reality, most snakes have components of both.

Hemotoxic means that the components in the venom attack tissues, like in the spider example, such that the venom is breaking down the tissues of the victim in a pre-digestion process. Such venom can cause extensive damage to tissues, great pain, and cause death slowly over a period of time.

Neurotoxic venoms act upon the nerves system, disrupting the ability of the nerves to send and receive messages. The effect of this kind of venom is that critical nervous system signals stop, such as the signal to your lungs to breath, or to your heart to beat. This kind of venom can act very quickly to cause death.

The vipers, the rattlesnakes, copperheads, cottonmouth in North America, have venom that is mostly hemotoxic, with lesser amount of neurotoxic components. The elapids, the coral snake in North America, and its relatives like the cobras, have venom that is mostly neurotoxic.

So now you can be erudite at parties when friends say things like “Watch out, that black widow you are about to sit on it poisonous!” You can smile politely as you sit, and say “Actually, it is venomous. Let me tell you all about it.”

Boneblogger: Science and the outdoors

Exploring the natural world