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Paleontology

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By Elof Carlson

Fossils are relatively rare because most of the animals and plants that have died in nature have been eaten or decomposed. Fossils are often found in sedimentary rocks, and those dead organisms were buried after drowning, caught by volcanic ash, buried in a mudslide or sucked down by quicksand or some other event less likely than falling on a field or in the underbrush of a forest, or left as scattered bones by hungry predators. Only in the past few ten thousand years have humans buried their dead, improving the chances that their remains will someday be unearthed and studied by paleontologists.

DNAUntil the last half of the twentieth century, the only way to use human fossils to work out a historical association was through comparative anatomy and a variety of chemical and physical tools to determine the age of the sediments in which they were unearthed. The idea of a paleogenetics arose in 1963, with the use of that term by Linus Pauling and his colleagues, who studied the amino acid sequences in hemoglobin molecules of numerous organisms, from sipunculoid worms to humans, that use hemoglobin to carry oxygen to body tissues.

In 1964, the first sequence of fragments of the DNA of an extinct quagga were worked out using the skin of an extinct specimen in a museum. The quagga was an animal that looked like a chimera of giraffe and a zebra.

Once DNA sequencing was worked out, especially by Fred Sanger and his colleagues, viruses, bacteria, single-celled organisms, and then more complex worms and flies were sequenced. By 2000, the human genome was being worked out. Svante Pääbo and his colleagues are leaders in the working out of fossil human DNA.

This is what has been found so far. Four contenders for species status lived about 40,000 years ago. Three populations of humans arose after an initial origin in Africa. Of these three, the Neandertals (Homo neanderthalis) left Africa earlier than our own Homo sapiens. The Neandertals were named for the Neander river valley where they found in Germany. We were named by Linnaeus as Man (Homo) the Thinker (sapiens).

Two additional populations were found, one in western Siberia and the other in Indonesia. The Siberian humans are called Denisovans (Homo denisova). They were named for the Denis cave in which they were found and they also had an exit from Africa. The Indonesian humans are called Homo floresiensis and are named for the island Flores in Indonesia where they were found. Where they came from is not yet known. They are unusual for their small size, a Hobbit-like three- and-a-half feet tall.

The DNAs of three forms of humanity have been sequenced. The complete sequence of DNA of an organism’s cell is called a genome. The Indonesian form went extinct about 12,000 years ago, but no DNA has been extracted from their remains. Neandertals and Denisovans went extinct about 40,000 years ago.

Analysis of the three available genomes shows that most Europeans have about 4 percent Neandertal DNA. Living people in Melanesia and Australian aborigines have about 4 percent H. denisova DNA. About 17 percent of Denisovan DNA is from Neandertals. The human branch Homo bifurcated and one branch split into H. neanderthalis and H. denisova. The other branch from Homo produced us, H. sapiens. We are 99.7 percent alike for H. sapiens and H. neanderthalis.

Since we have 3 billion nucleotides to our genome, there remain 9 million mutations between us, most of it in our junk DNA. There are, nevertheless, hundreds of gene differences between our two species. It also means that where these populations came into contact, fertile matings occurred, and remain in our DNA from our ancestral “kissing cousins.”

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

Studying parts of dinosaur bones that are smaller than the width of a human hair, Michael D’Emic specializes in sauropods, which includes the long necked Brontosaurus. Photo from SBU

They didn’t mark the wall in crayon or pencil with a date to monitor how they grew, the way parents do in suburban homes with their children. Millions of years ago, however, dinosaurs left clues in their bones about their annual growth.

Dinosaur bones have concentric rings, which are analogous to the ones trees have in their trunks.

A diagram represents the growth rings in dinosaur bones. Image from Michael D’Emic and Scott Hartman
A diagram represents the growth rings in dinosaur bones. Image from Michael D’Emic and Scott Hartman

Michael D’Emic, a paleontologist and Research Instructor in the Department of Anatomical Sciences at Stony Brook, studied these bones and the size of these rings and concluded that dinosaurs were warm-blooded.

In a paper published in the journal Science, D’Emic demonstrates how the growth rates of these bones indicate dinosaurs were much more like birds than reptiles in their metabolism.

“This supports the idea that dinosaurs were warm-blooded,” said Holly Woodward Ballard, an Assistant Professor of Anatomy in the Center for Health Sciences at Oklahoma State University.

D’Emic re-analyzed data that appeared in a 2014 Science article, in which other scientists had suggested dinosaurs were mesothermic, which is somewhere in between cold blooded organisms, like reptiles, and warm-blooded creatures, like birds, three-toed sloths, and humans.

D’Emic was on a dinosaur dig in Wyoming when the paper came out last June. When he returned to Stony Brook in July, he took a closer look at the results. “When I read the paper, I thought they hadn’t accounted for a couple of factors that would bias the results,” he said. “I was curious how changing some of those factors” would affect the conclusions.

D’Emic studies the smallest parts of bones. Indeed, for creatures that lived millions of years ago and weighed as much as 40 tons, he looked closely at cells that were a fraction of the width of a human hair.

In his approach to the data, D’Emic adjusted for seasonal growth patterns. Typically, dinosaurs grow only half the year. In the other half, when food is scarce or the temperature drops enough, the dinosaurs would have needed that energy to survive. When he accounted for this, he said the rate of growth doubled.

Comparing his estimated growth rate for dinosaurs with the rate for mammals and reptiles of similar size suggested the dinosaurs  “fell right in line with mammals,” he said.

Michael D’Emic enjoys a Lord of the Rings moment in Beartooth, Wyoming, near an excavation site in 2010. Photo from D’Emic.
Michael D’Emic enjoys a Lord of the Rings moment in Beartooth, Wyoming, near an excavation site in 2010. Photo from D’Emic.

A dinosaur’s metabolism could affect life histories including how the dinosaurs raised their young, as well as elements to their physiology, he said. “Such a fundamental aspect of an organism has implications for the kind of animals we expect them to be,” he said.

D’Emic recognizes that some paleontologists will question his conclusions about dinosaur metabolism. When looking at a broad group of paleontologists, he “still finds a pretty big spectrum of ideas” about metabolism and the “debate is probably still open.” After this recent work, D’Emic reached out to partners from around the world to explore bone growth in other groups of dinosaurs.

Ballard, who studies the growth and development of Maiasaura (duck-billed) dinosaurs from hatchling to adults primarily in Montana, supports D’Emic’s conclusions. She said his analysis will reinforce some of the hypotheses she had about dinosaur metabolism. Ballard said D’Emic was “well thought of” and has“definitely made an impact in the histological field.”

When he was in high school, D’Emic had the opportunity to join a dinosaur dig in New York, where he found a mastodon tusk. He was living in Manhattan at the time and went to Hyde Park with a summer class. After two weeks at the site with the class, he asked if he could come back, and wound up returning regularly for months, until school started.

“I didn’t want to go back to high school when September rolled around,” D’Emic recalled.

D’Emic, who recently left a dig in Utah and was on his way to join other Stony Brook researchers in Madagascar, said he still feels inspired by the opportunity to learn about dinosaurs. When he came to the University of Michigan in 2006 to start his PhD program, he planned to focus on Titanosaurs. By the time he left, the number of species of Titanosaurs scientists had discovered and categorized had doubled.

“It’s a cool time to be a paleontologist,” he said.