Molecular paleontology

Molecular paleontology involves recovering deoxyribonucleic acid, proteins, and other molecules from ancient animal, human, and plant remains for study and classification. Previously, science believed that an organism's fossilized remains retained little molecular information. However, molecular fragments are often found in such remains, primarily because of advances in research practices and technologies.

Basic Principles

Molecular paleontology involves extracting and studying ancient human, plant, and animal remains. This practice includes the examination of deoxyribonucleic acid (DNA, which carries the genetic information of an organism), lipids (fats), carbohydrates, and other molecular-level materials found in the fossilized remains of ancient humans, dinosaurs, and florae. This pursuit is made easier by discovering actual soft tissues, bones, and other components. Scientists long presumed that such materials were destroyed in the fossilization process and could not yield valuable information. However, technological improvements have enabled scientists to extract usable subcellular materials from crystallized bone from animal and early human remains.

Molecular paleontology is part of a broader attempt to understand how life on Earth has evolved. Paleontologists search through strata layers of the Earth for the fossilized remains of plants and animals (including proto-humans). Molecular paleontologists use the remains to uncover the genetic composition of these organisms. Using the latent materials in the tissue or fossilized remains, scientists may, for example, piece together the genetic profiles of long-extinct organisms and their respective similarities and differences from modern species (a field known as phylogenetics). Scientists also may use such information to study the origins and transmission of certain diseases.

Background and History

In any science, a theory cannot progress into fact without concrete evidence, particularly without evidence that may be independently verified. One of the greatest challenges facing paleontology—the study of life during prehistoric periods using fossilized remains—is that the evidence needed to support a theory likely disappeared millions of years ago. Paleontologists have learned a great deal about dinosaurs, prehistoric plants, and even the earliest humans by assembling the bones and fragments buried under the strata or by studying the fossilized remains of such life forms that have been etched into solid rock. Until the mid-1950s, however, it was presumed that DNA, amino acids, or other molecular-level genetic material could never have survived fossilization.

In 1956, however, renowned American geochemist, geophysicist, and molecular biologist Philip Abelson dissolved a piece of a fossilized stegosaurus (a dinosaur from the late Jurassic period) in hydrochloric acid. He reported that from that solution, he found small amounts of amino acids—simple compounds that serve as the building blocks of protein. Two decades later, several scientists used Abelson's principles to analyze the ability of certain prehistoric organisms to combat infections. In the 1980s, molecular paleontology was used to build on this immunological study, citing similarities between species' ability to create antibodies (which help an organism fight foreign cells and invading viruses). Based on this and similar studies, scientists uncovered many evolutionary connections between prehistoric and modern species that might otherwise have gone unconfirmed.

Tissue Analysis

There are two general scenarios in which molecular paleontology is made possible. The first is through the analysis of actual tissue. For example, during the Pleistocene period (between 1.8 million and 100,000 years ago), woolly mammoths thrived in the permafrost of the cold Eurasian regions. Eventually, the species became extinct, but scientists have found several woolly mammoths encased in the ice of present-day Siberia (and elsewhere). A question that has vexed paleontologists for decades before these creatures were uncovered was how an animal originating in much warmer climates (in locations now populated by elephants) could survive after migrating north. Experts theorized that the answers lie in the creature's blood, specifically that the mammoth's blood contained some special element that enabled oxygen to travel quickly through its large body in cold temperatures. However, although the mammoth's tissue might still exist, its blood would have disappeared long ago.

Still, when paleontologists unearthed frozen mammoth carcasses in northern Siberia, these scientists could extract amino acids and DNA from the tissue samples. Using a chemical compound known as a blood substitute, the scientists re-created the mammoth's hemoglobin (which carries oxygen through the bloodstream). After careful genetic analysis, the molecular paleontologists determined that the mammoths had undergone a significant mutation, allowing them to use different amino acids to cope with the dramatic changes in their environment. The implications of this finding are significant: Scientists believe that, based on this discovery, it may be possible to create new artificial blood products for persons placed in a state of hypothermia for brain and heart surgeries.

Tissue samples taken from frozen woolly mammoth carcasses often provide invaluable information about the creatures, but it has been much more difficult to locate the tissue samples of dinosaurs. Indeed, the dinosaur bones and fossils unearthed by paleontologists are often hundreds of millions of years old. Although rare, there have been instances in which small amounts of tissue have been found deep in the bones of dinosaurs.

In 2005, for example, paleontologists made such a find inside one of the bones derived from one of the most prized finds in paleontologya Tyrannosaurus rex (or T. rex) unearthed in 2003 in Montana. A femur recovered at the site actually contained the remains of soft tissue and collagen (a protein that serves as the building block for connective tissue). Scientists removed the collagen and analyzed the protein sequences (the order of amino acids that form a polypeptide chain, which in turn forms part or all of a protein molecule). The researchers then compared the protein sequences of the T. rex with those of modern animals, confirming what paleontologists have for many years suspected but were never able to verifysome dinosaurs bore more similarities to birds, particularly ostriches, and chickens, than to modern reptiles. This project represented the first time that molecular data placed a nonavian (birdlike) species along the evolutionary scale for birds.

Crystallized Remains

The second area in which molecular paleontology is possible is much more difficult to employ, as it involves the extraction of crystallized fragments of amino acids from fossils instead of from soft tissue. DNA degrades quickly after an organism dies. When an organism dies and is ultimately buried under the soil, the DNA on the bone becomes degraded and potentially contaminated by other DNA. However, scientists have discovered that crystallized cells may be found within the collagen in fossilized bones. Placing ground bone powder into a solution of sodium hypochlorite, scientists extracted strings of DNA from the clumps of crystals. These strings were found reproducible, enabling scientists to create a more complete genetic profile of the organisms in question.

The implications of such a finding are significant. By analyzing the DNA of early organisms, scientists can research their migratory patterns, how they reacted to disease, and how they were genetically related to other organisms (including those living now). However, there is a risk involved with this new procedure. Reproducing DNA strands based on the fragments found within bone may be possible, but it may yield unreliable data. Still, many scientists believe this approach creates results that are as authentic as possible.

Electron

Electron microscopes can magnify images by as much as several hundred thousand times, with an image clarity and depth that can reveal not only molecular-level objects, but also their composition. An electron microscope focused on a sample can produce images that provide clues about that object's origins and similarities to other organisms. For example, in 1997, scientists used an electron microscope to study fossilized spores from prehistoric mushrooms. The microscope revealed the spores' distinctive shapes and surface textures, which, when compared with other similar spores, revealed how the mushrooms migrated during continental drive.

Electron microscopes are also quite useful for analyzing crystals buried within dinosaur bones. In one study of sauropods (a class of large, four-legged dinosaurs that includes Brontosaurus and Brachiosaurus), molecular paleontologists used an electron microscope to analyze the crystal patterns within the bones of juveniles and adults. The images the microscope produced showed a diverse grouping of crystals in the juvenile, confirming a theory that young sauropods had a wide range of crystals within their bones that enabled them to perform certain mechanical functions with greater ease.

Spectrometry

Spectrometry involves using a device (the spectrometer) to emit light, sound, or particles onto an object under study. Spectrometers then record the object's reaction, such as the quantity of light it absorbs or the energy it itself projects upon exposure. Spectral analysis has proved extremely useful in discovering the physiological makeup of certain organisms.

Some scientists, for example, believe that certain organic substances, such as blood and bone cells, can, under the right conditions, survive in fossilized remains. One paleontologist, who was studying a slice of bone from a T. rex as a graduate student in 1992, noticed what appeared to be ancient blood cells. In an effort to confirm her findings, she subjected the sample to a laser spectrometer to detect heme (a molecule that contains iron found in red blood cells). Heme is known to absorb a distinctive amount of light when exposed. Indeed, her theory was confirmed when the sample was exposed to the spectrometer. The object she had found was indeed a red blood cell.

Two types of spectrometers occasionally used in molecular paleontology are the inductively coupled plasma atomic emission spectrometer (ICP-AES) and the electrothermal atomic absorption spectrometer (EAAS). The ICP-AES involves targeting energy emissions at an object (after it has been immersed and dissolved in an acidic solution) in the hope that certain elements in the sample will react and emit energy along a certain wavelength. The EAAS focuses a beam of ultraviolet light through a flame, using a detector to capture the elemental response along a certain wavelength. Each type of spectrometer is primarily focused on the search for metals, such as iron and sodium. It is, therefore, useful in pursuing many of the fundamental elements found in blood and related tissue. However, both spectrometers are expensive to use in molecular paleontology, which has limited their application in this field.

Chemical Analysis

As Abelson demonstrated in his 1950s experiment, chemistry is invaluable in pursuing DNA and other molecular remnants within fossilized organisms. Chemical compounds have proved highly effective in breaking down the elements of fossilized bone and rock, making it easier to detect and extract important evidence. For example, in 2004, scientists in China analyzed the skeletal fossils of four dinosaurs in China's Sichuan Province. Rather than employ ICP-AES or ETAAS, the molecular paleontologists immersed samples of the fossils in a bath of boiling water and a highly corrosive combination of hydrochloric and nitric acid known as aqua regia. After the fossil samples were digested, the scientists detected and recorded large quantities of arsenic molecules. The presence of this toxic substance in the creatures' bones provided some clues as to why dinosaurs died in Sichuan specifically and why they died perhaps elsewhere.

Relevant Organizations and Institutions

Molecular paleontology serves a significant purpose in two general areas. First, science attempts to answer many questions about the forms of life that existed on Earth in the prehistoric eras. Second, science seeks to determine how those organisms ceased to exist or evolved into modern-day plants, animals, and mammals. Many groups and organizations also play significant roles in the field of molecular paleontology.

Because paleontologists and molecular paleontologists conduct scientific research and experimentation, they frequently work in major universities' zoology, biology, or paleontology departments. Here, they conduct experiments, study fossil contents, collate data, and produce scientific papers and hypotheses.

Museums play a major role in paleontology, largely because so many fossilized remains of dinosaurs, plants, and other prehistoric organisms are housed and preserved at such institutions. Most museums are supported by donors and admission fees, which are used to contribute to research. Universities support some museums. The Museum of the Rockies, for example, has one of the world's largest collections of dinosaur fossils and is affiliated with Montana State University.

Governments play an important role in paleontology and molecular paleontology. Primarily, government agencies, such as the National Science Foundation, provide grants and support to help scientists perform their respective research. Such support includes funding for equipment (including spectrometers) and funding for travel to remote sites. Because molecular paleontology is a relatively new field, the National Science Foundation is positioned to invest significantly in such high-risk, high-payoff research.

Implications and Future Prospects

Before the 1950s, many considered paleontology a branch of geology. However, with time, paleontology began focusing on studying ancient life rather than on the fossils into which ancient life evolved. Molecular paleontology is a continuation of this changing attitude. This approach adds a new dimension to science, utilizing the twenty-first-century understanding of genetics and biodiversity and the latest technology.

Molecular paleontology uses many techniques, including state-of-the-art technology (such as spectrometers and electron microscopes). However, using such systems is sometimes cost-prohibitive, especially for nonprofit museums and universities. As a result, the high price of using the technological tools of molecular paleontology could limit the field's growth.

Paleontology has many implications for modern science. Some scientists, when attempting to predict how life in the modern world might react to global warming and other climate changes, consider how organisms adapted genetically to climate changes during prehistoric times. As technology and research techniques evolve, molecular paleontology will continue to be relevant to the study of life on Earth.

Molecular paleontology research achieved several important milestones in the first quarter of the twenty-first century. Scientists began sequencing DNA from Neanderthals in 2006, and in 2013, the Neanderthal genome project published the first entire Neanderthal genome. In 2021, molecular paleontologists recorded DNA from a Siberian mammoth's tooth preserved in permafrost for 1.6 million years. It was the oldest DNA to be sequenced at the time of its sequencing and the first DMA sequenced from animal remains.

Principal Terms

amino acid: a simple compound that serves as the building block of protein and, therefore, the development of all organic life on Earth

collagen: a protein that is a building block for connective tissue

DNA (deoxyribonucleic acid): the nucleic acid that carries the genetic information of an organism

phylogenetics: a field of study in which the genetic profiles of long-extinct organisms are determined and their respective similarities and differences from modern species are established

protein sequence: the order of amino acids that form a polypeptide chain, which in turn forms part or all of a protein molecule

Bibliography

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