Stories tagged Diversity of Organisms

Sep
19
2011

According to their website, National Fossil Day is a "celebration organized to promote public awareness and stewardship of fossils, as well as to foster a greater appreciation of their scientific and educational value." This year the celebration is set for October 12, and like last year, I'll probably be doing several posts regarding fossils and the event itself over the next couple of weeks. So with that in mind, here's my first contribution.

Skull of Amia uintaensis (bowfin): Large and well-preserved fossil fish from Fossil Lake deposits shows fine detail, including scales and skin. The full fossil is 49 inches in length. Science Museum of Minnesota collection.
Skull of Amia uintaensis (bowfin): Large and well-preserved fossil fish from Fossil Lake deposits shows fine detail, including scales and skin. The full fossil is 49 inches in length. Science Museum of Minnesota collection.Courtesy Mark Ryan
Tucked in a corner of the Dinosaur and Fossils Gallery here at the Science Museum of Minnesota is a display of fossil fish from the famous Green River Formation. The display offers visitors a look at some of the most well known fossils in the world. Visit a rock shop, natural history store, souvenir shop, or museum just about anywhere and you’ll find fish fossils from the Green River Formation for sale. Literally millions of fossils have been extracted from the formation, so it’s no surprise at all to find some in our paleontology gallery. The display represents only a fraction of the Green River fossils in the Science Museum of Minnesota collection.

Fossil Butte: The butte stands in Fossil Butte National Monument and represents the ancient deposition remains of the center of Fossil Lake in western Wyoming. Limestone and mudstone layers near the top of the butte are rich in fossil fish and other fauna and flora from the Eocene Epoch.
Fossil Butte: The butte stands in Fossil Butte National Monument and represents the ancient deposition remains of the center of Fossil Lake in western Wyoming. Limestone and mudstone layers near the top of the butte are rich in fossil fish and other fauna and flora from the Eocene Epoch.Courtesy Mark Ryan
The sources of this splendid array of extraordinary fossils are the deposits left by three freshwater lakes that existed around 50 million years ago during the Eocene Epoch. These ephemeral bodies of water existed across 17 million years of time, and not all at the same time. Lake Gosiute was the largest in area with a diameter of about 200 miles. Lake Uinta had the most surface area and was the shallowest and existed the longest. Fossil Lake was the smallest and the shortest-lived – but the deepest. The lakes existed in a subtropical environment flush with all sorts of animal life from insects to mammals. More than 20 species of fish populated the waters while crocodiles, turtles and other reptiles basked along lake shores lined with lush forests of palm and fig trees. Birds and bats flew through the sky. Ferns sprouted in the shadowed woodlands of oaks and maples that grew up the slopes of the surrounding mountains. Fir and spruce trees existed in the higher elevations. Fossil remains from this past life are found in all of the basins where the three lakes once existed, but Fossil Lake, as its name implies, produces the most abundant Green River Formation fossils, especially fossil fish.

Fossil Butte: The rich fossil deposits were first discovered by workers for the Union Pacific Railroad.
Fossil Butte: The rich fossil deposits were first discovered by workers for the Union Pacific Railroad.Courtesy Mark Ryan
Railroad workers helping expand the Union Pacific railroad in the mid-1800s first discovered the fossil deposits near the town of Green River, Wyoming. The discovery soon drew the attention of scientists. A geologist named Dr. John Evans collected some of the first fossils from the region in 1856, and Philadelphia paleontologist, Joseph Leidy, soon after described for the first time, Knightia eocaena, the most common fossil fish found in the formation. Edward Drinker Cope, another paleontologist, also collected from the deposits and wrote several important papers starting in 1870.

Heliobastis radiens: A stingray found in the Green River Formation deposits. Science Museum of Minnesota collection.
Heliobastis radiens: A stingray found in the Green River Formation deposits. Science Museum of Minnesota collection.Courtesy Mark Ryan
The fossils on display at the Science Museum include Amia, Knightia, Diplomystus, and the exquisite stingray Heliobatis all preserved in buff-colored slabs consisting of soft lamination of mudstone, limestone, and volcanic ash. There’s also a slab of garfish, and an unlabelled predator named Priscacara next to the large palm frond on the wall near the entrance. Lance Grande (a graduate of the University of Minnesota and paleontologist at the Field Museum of Natural History in Chicago) is considered the leading expert in the fossil remains found in the Green River Formation. His book Paleontology of the Green River Formation (which I referenced heavily for this post) is considered a classic, and contains photos of many specimens found in the Science Museum’s collection.

The two main fish-bearing units in the strata are the 18-inch Layer and the Split-Fish Layer. The formation is considered a laggerstatte (which means storage place) where nearly an entire ecological system is finely preserved in the fossil record. Several lagerstätten exist around the world but the Cambrian-aged Burgess Shale in British Columbia, and the Late Jurassic-aged Solnhofen quarry in Germany are probably the two best known.

Green River Formation: Strata of the famed fossil-rich formation visible in Fossil Butte National Monument. The butte represents deposits from what was once the center of Fossil Lake that existed 50 million years ago during the Eocene Epoch in what is now western Wyoming.
Green River Formation: Strata of the famed fossil-rich formation visible in Fossil Butte National Monument. The butte represents deposits from what was once the center of Fossil Lake that existed 50 million years ago during the Eocene Epoch in what is now western Wyoming.Courtesy Mark Ryan
The deposited remains of what used to be the center of Fossil Lake today form a high butte in western Wyoming that towers a thousand feet above the Visitor Center at Fossil Butte National Monument. The monument was established in 1972 and is located 9 miles west of Kemmerer, Wyoming in the extreme southwestern corner of the state. Despite its somewhat isolated location, it’s well worth going out of your way to see.

Abandoned workers' shelter: Historic Quarry at Fossil Butte National Monument.
Abandoned workers' shelter: Historic Quarry at Fossil Butte National Monument.Courtesy Mark Ryan
My brother Pat and I visited the area on one of our recent geo-trips out west. We first stopped at the Fossil Butte visitor center where, not surprisingly, some extremely rare and high quality Green River fossils were on display, including insects, lizards, turtles, crocodiles, birds, bats, and other mammals. Finely preserved fossils of leaves, cattails, flowers and fruit are also on display. We watched a short film explaining the area and the fossils found there, then Pat and I headed out to a nearby abandoned fossil quarry within the park for a bit of exploration on our own. We parked in the designated lot just off the highway, grabbed our packs and some water, and began our ascent to the Historic Quarry. The climb along the 2.5 mile hiking trail was no picnic – it took about an hour to get to the top, but information signs dot the trail to guide and inform you as you go along. Historic Quarry: Pat Ryan stands level with the fossil-rich 18-Inch Layer located in the abandoned quarry at the top of Fossil Butte.
Historic Quarry: Pat Ryan stands level with the fossil-rich 18-Inch Layer located in the abandoned quarry at the top of Fossil Butte.Courtesy Mark Ryan
And the view of the wide Wyoming landscape is breath-taking. The main trail eventually runs parallel to the butte and along that stretch is an a-frame shack used by workers who excavated the quarry back when it was still operating. Every once in a while we’d come upon a slab of rock that had fallen from the fossil layer above. You could tell this by its buff color, plus one we examined contained the partial remains of the head of a Diplosmystus. The regular hiking trail took us about 600 feet above the highway, but to get to the 18-inch Layer we had to take a spur trail another couple hundred feet up above that.

The 18-Inch Layer exposed at Fossil Butte's Historic Quarry: Fossils from this layer of the Green River Formation are exhibited in museums all over the world.
The 18-Inch Layer exposed at Fossil Butte's Historic Quarry: Fossils from this layer of the Green River Formation are exhibited in museums all over the world.Courtesy Pat Ryan
The 18-inch Layer contains some of the best preserved fossils in the world, and is composed of limestone, oil shale, and volcanic ash. The lacustrine (lake) deposits are laid out in alternating pairs (varves) of light and dark layers each representing an annual cycle of sedimentation. Overall there’s about 4000 years of deposition represented in the layer. Three feet beneath the 18-inch Layer (but not exposed at the Historic Quarry) is a second major fossil unit named the Split Fish Layer (or sandwich layers). This unit is about 6-1/2 feet thick and is so called because when the rock is separated, the fossils themselves split between the top and bottom layers diminishing the quality. When the layers of the 18-inch Layer are separated the fossils are found on only one sheet and protected under a layer of matrix that has to be expertly removed. The Split Fish Layer fossils usually need little if any preparation. According to Fossil Butte museum curator, Arvid Aase, there actually exists several so-called split fish layers, three of them above the 18-inch Layer, along with what are called a mini-fish layer and gastropod bed.

The fossilization process that occurred in the Green River Formation is unique in that the lakes contained a nearly perfect and ideal environment for preserving the delicate remains of its biosphere. A constant rain of calcium carbonate suspended in the waters insured that any dead creature or plant lying on the bottom would be covered and protected from bacteria or the elements. The deeper waters were probably anoxic – meaning lacking oxygen – which aided in further protecting the remains. The fossils are wonderfully preserved, showing fine skeletal details, scales, skin, and even feathers in some cases, all preserved as delicate carbon traces of the once living entity.

Knightia eocaena: The most common genus of fish found in the Green River Formation. Remains are sometimes found in mass mortality layers such as shown here. Science Museum of Minnesota collection.
Knightia eocaena: The most common genus of fish found in the Green River Formation. Remains are sometimes found in mass mortality layers such as shown here. Science Museum of Minnesota collection.Courtesy Mark Ryan
It’s thought that algal blooms sometimes occurred in the lakes during the warmer seasons resulting in mass mortalities of thousands of fish. Large slabs containing more fossil fish than you can count are still being mined from the area.

When I’m working my Tuesday afternoon shift in the Dinosaur and Fossils gallery at the museum I often carry with me a Green River Formation fossil of a leaf to share with visitors. I’ll scratch the matrix with a key or fingernail to allow visitors to experience the oily odor that that emanates from within the rock. Actually the odor is from kerogen a bituminous organic compound in the rock that serves as a source for oil shale, considered a substitute for crude oil. The Green River Formation contains the largest oil shale deposits in the world greatly exceeding the oil reserves of Saudi Arabia.

Be aware that since the Historic Quarry trail is part of Fossil Butte National Monument, collecting of any kind of fossils is prohibited within its borders but fortunately several commercial operations in the area allow you to enter a quarry for a fee and dig up your very own fossils to take home. I’ve never done this so I can’t vouch for any of these commercial dig sites but I am including some links below for some of the more well-known ones in the area.

But even if you can’t make it out to Fossil Butte National Monument this year, you can still come the Science Museum of Minnesota and see our collection, or visit a natural history museum in your own area. Chances are they’ll have some fabulous Green River Formation fossils on display to share with you.

SOURCE and LINKS
GRF info at the Virtual Fossil Museum
Collection and preparation of fossil fish
Historical Geology of the GRF
Ulrich Quarry Fossil Gallery
Warfield Fossil Quarry

Sep
11
2011

There I was, sitting on my back porch enjoying the last days of summer, when I heard a sound--"zzzzzZZZZzzzzz"--first once, then again, and finally a third time in short succession. I heard coming from the trees the songs of the cicadas.

The cicada is a large (1-2 inches long) insect with a rather scary looking appearance.

The name cicada comes from Latin meaning "tree cricket" and while they aren't directly related to crickets, they are just as harmless.

About two weeks ago, as I was carrying something out to my car, I noticed a cicada in the process of shedding its exoskeleton to become an adult. You see, a cicada spends years underground as a nymph, feeding on the roots of various plants. After a certain number of years pass by (13 for some, 17 for other species) they emerge from their earthen nursery and climb up the nearby plants to get out of the reach of predators. Afterward, they molt their larval exoskeleton and become an adult. I couldn't believe my luck to have a cicada molting before my very eyes.

When I first noticed it, I saw something pink hanging from my tree. The exoskeleton had already split down the back and the newly adult cicada was climbing out of its old shell, all pink with spring green wings instead of black or brown. Initially, the wings were small green bumps on its back, but as they dried, the wings extended to their normal size. I was disappointed that I couldn't stay and watch its color change while the exoskeleton hardened, because that would also have been cool to see.

Cicadas are a rather delicate and sensitive insect. If the environmental conditions aren't just right with regards to pollution, acidity and temperature, when they emerge the cicadas will be deformed and often sterile. With this in mind, remember that while they might appear to be scary-looking, cicadas are quite harmless and actually a natural sign that the area in which you live is healthy.

Image courtesy of Bruce Marlin
Image location http://en.wikipedia.org/wiki/File:Magicicada_species.jpg.

Aug
06
2011

Archaeopteryx (Thermopolis specimen): Has the iconic transitional fossil had its feathers ruffled by a recent discovery? Not really.
Archaeopteryx (Thermopolis specimen): Has the iconic transitional fossil had its feathers ruffled by a recent discovery? Not really.Courtesy Mark Ryan
China has been producing some remarkable and groundbreaking dinosaur fossils in recent years that have caused paleontologists to reconsider long-held views. A recently described feathered dinosaur is no different. Xiaotingia zhengi, discovered in the Jurassic shales of the Liaoning Province, has been in the news lately because it supposedly knocked the well-known, so-called proto-bird Archaeopteryx from its perch as the earliest bird.

The study by paleontologist Xu Xing and his colleagues from the Chinese Academy of Sciences in Beijing appears in Nature. Their research, it seems, has determined that Xiaotingia and Archaeopteryx share many features that make the two of them more bird-like dinosaurs than dinosaur-like birds. Do you see the difference there? I guess I do. Anyway, essentially what it means is that Archaeopteryx has been pushed back a little and is just a bit more distantly related to birds than previously thought. The classification places both Xiaotingia and Archaeopteryx in with avian-like carnivorous dinosaurs such as deinonychosaurs, dromaeosaurids, and troodontids. The recent spate of fossils coming out of China can’t help but alter some our old views of the middle to late Jurassic fauna. Many dinosaurs (including non-avian ones) living during that time were equipped with bird-like features: e. g. long arms, feathers, wishbones, etc. They were all over the place.

But all you diehards out there in the Archaeopteryx-is-a-bird camp need not despair just yet. Dr. Xu himself admits that some of the conclusions in the study are based on pretty weak evidence. Archaeopteryx continues to rank as an exceptional transitional fossil (along with Xiaotingia). Its place in the transition has just shifted slightly, that’s all. Further studies and new fossils will no-doubt shake up the branches of the avian family tree again.

References:
Story at Pharyngula
New York Times story

May
23
2011

Tibicen linnei: An annual cicada
Tibicen linnei: An annual cicadaCourtesy Bruce Marlin (via Wikipedia Creative Commons)
Summer is heading our way and soon the familiar buzzing of cicadas will fill the air. But for some, particularly in the southern and eastern United States, the buzz will become a loud symphony of sound. That's because, this year, the Great Southern Brood will (actually already has in some places) reappear and millions of the insects will soon be crawling out of the ground to overwhelm us with their vast numbers and cacaphonic chorus.

Relax. Last weekend's rapture was a bust (or was it?), and there’s nothing to worry about in the biblical sense. It’s merely the latest appearance of Magicicada neotredecim and M. tredecim, two closely related species of cicada that show up every 13 years in the United States to fill the treetops with their buzzing song.

The most common genus of cicadas in the US is Tibicen and unlike Magicicada, cicadas in the genus Tibicen appear annually, not periodically. After a 2-3 year stint as nymphs, Tibecen cicadas emerge into their adult stage. The full-grown insect measures about 1-2 inches in length with long translucent wings and distinctive green, brown, and black markings on the middle of its body. Generations overlap so they show up every year and can be heard in many areas, including Minnesota, during the hot and steamy Dog Days of summer buzzing to high heaven. It’s that shrill, grating noise that builds in the air and sounds like someone is cutting up cement blocks with a chainsaw. As deafening as it can be, I like the sound, in much the same way I like the smell of rotting leaves in the fall, it triggers memories.

But I’m not sure how I’d feel about Tibicen's cyclical cousins - those belonging to the Magicada genus - that show up all at once in mass periodical emergences and put on huge choruses of buzzing. There are seven species that do this in the US, three in 13-year cycles, and four in 17-year cycles. Periodical cicadas are categorized into broods numbered in Roman numerals from I to XXX. The thirteen-year cycles occupy XVIII–XXX; seventeen-year cycles number I–XVII. Only about 15 broods are still recognized. There are still only seven cyclical species but some species emerge happen at different times in different regions, hence the number of broods. This year it will be a 13-year cycle called Brood XIX , and it is the largest of the 13-year cycles in terms of geography.

The numbers involved in a periodical swarm are huge but, as Vanderbilt biologist Patrick Abbot explains, the vast numbers increase the possibility of available mates and serve as a way to overwhelm the cicadas many predators, which include birds, snakes, turtles, spiders and wasps, and even fungi. It’s interesting that the periodical emergences have evolved into separate prime number cycles. The reason is probably to reduce competition between broods.

“Say you have two populations, one which emerges every five years and one which emerges every 10 years. Then they would emerge simultaneously every 10 years," Abbot said. "Whereas the period between simultaneous emergences between populations with 13- and 17-year cycles is 221 years."

Occasionally, two cyclical broods have been known to emerge simultaneously but usually the overlap is minimal. For example two 13-year broods rising at the same time but in adjacent regions.

During a brood’s synchronized emergence the number of individuals can be daunting. Some emergences have been estimated to contain something like 1.5 million cicadas per acre of land. That amounts to 800 tons (!) of biomass busily buzzing within a square mile of forest. Think of that!

But despite the huge numbers involved in a cyclical emergence, cicadas are pretty harmless, and don’t voraciously eat up crops like locusts do, nor do they sting or bite. The most damage done is by females when they make “v”-shaped slits in the bark of a twig to lay their eggs (I suppose this could feel like a sting if she mistakes your arm for a tree branch). But, come on, even this is nothing compared to a plague of locusts wiping out the summer corn crop.

The word cicada is Latin and means “buzzer” Very apropos, don’t you think? The males of the species spend a lot of time trying to get the attention of female cicadas by vibrating a membrane on their exoskeleton called tymbals. Each time the muscles contract or relax the tymbals they produce a click. Portions of the exoskeleton such as the abdomen or thorax help amplify the sound. The rapid vibration causes a shrill and (possibly annoying) buzzing, and each of the world’s estimated 2500-3000 species has its own distinct sound. The females, by comparison, make a rather boring click with their wings to attract males (I suppose the male cicadas don’t think it boring). You can replicate the female clicking by snapping your fingers in rapid succession a couple times.

When periodical cicada eggs hatch the nymphs drop down and burrow deep into the ground where they spend most of their lives sustaining themselves for several years ingesting fluids from tree roots and developing through five juvenile stages. Scientists suspect soil temperature triggers the emergence. When it reaches 64 degrees F., the nymphs head for the surface. It seems the likely catalyst since emergences in warmer, southern regions take place sooner than those farther north. Whatever the case, when they do emerge, the nymphs crawl up and attach themselves to nearby vegetation where they eventually molt out of their skins. They don’t begin adult activities until after their exoskeletons harden. So for the first 4 to 8 days after molting, they pass through a stage called teneral (meaning soft and tender) before the exoskeleton is complete. The adult stage of a cicada lasts anywhere from a couple weeks to a few months. Very short in comparison to their other life stages.

People eat cicadas in several areas of the world. And the females are meatier and more desired. I suppose the insect is a good source of protein but – there’s no way I’m ever doing that - I’d never eat one. Maybe I shouldn’t say “never”. Some Native American tribes supposedly survived times of famine by eating cicadas.

If you live in or are visiting an area that is or will soon be overrun by an invasion of the Great Southern Brood, rather than cowering in a corner and wailing and gnashing your teeth, head outside, go for a walk, and take in a symphony of cicada songs. While you’re out there enjoying the summer day, you can get even more involved by trying some of these neat cicada experiments. It will take your mind off the fact that you’re surrounded by 800 tons of buzzing biomass.

SOURCES and LINKS

Cicada Central
Magicicada.org
Vanderbilt release
Cicada Mania page

May
18
2011

R/V Hespérides, docked at Aloha Tower in Honolulu, Hawai`i
R/V Hespérides, docked at Aloha Tower in Honolulu, Hawai`iCourtesy C-MORE
How would you like to be aboard a ship, circumnavigating the globe, collecting samples from the world’s ocean?

That’s exactly what Spanish oceanographers are doing on their Malaspina Expedition aboard the Research Vessel, R/V Hespérides. Scientists and crew left southern Spain in December, reached New Zealand in mid-April, and recently arrived in Hawai`i. The expedition's primary goals are to:

  • build upon the historic 1789-1794 Malaspina expedition to promote interest in marine sciences among the Spanish public, particularly the nation’s youth
  • collect oceanographic and atmospheric data -- chemical, physical and biological – that will help evaluate the impact of global change
  • explore the variety of marine life, including microbes, especially those living in the deep sea
  • CTD: As this oceanographic instrument is lowered over the side of a ship, each gray Niskin “bottle” can be electronically triggered to collect a seawater sample from a different ocean depth.
    CTD: As this oceanographic instrument is lowered over the side of a ship, each gray Niskin “bottle” can be electronically triggered to collect a seawater sample from a different ocean depth.Courtesy C-MORE
    In connection with the latter two goals, the Malaspina scientists met with their colleagues at the Center for Microbial Oceanography: Research and Education (C-MORE). The two groups of scientists are working together. "We can exchange data on the local effects, what's happening around the Hawaiian Islands, and they can tell us what's happening in the middle of the Pacific," said Dr. Dave Karl, University of Hawai`i oceanography professor and Director of C-MORE.

    The Malaspina-C-MORE partnership is the kind of cooperation that can help solve environmental problems which stretch beyond an individual nation’s borders. The R/V Hespérides has now left Honolulu on its way to Panama and Colombia. From there, the scientists expect to complete their ocean sampling through the Atlantic Ocean and return to Spain by July. Buen viaje!

May
02
2011

the ocean's 5 major gyres
the ocean's 5 major gyresCourtesy NOAA
We often talk about the ocean ecosystem. And, indeed, there is really just one, world-wide ocean, since all oceans are connected. An Indian Ocean earthquake sends tsunami waves to distant coasts. Whitecaps look as white anywhere in the world. The ocean swirls in similar patterns.

However, oceanographers do find differences from place to place. For example, let’s take a closer look at the chemistry of two swirls, or gyres as they’re more properly called. Scientists have found a micro difference between the North Atlantic Gyre and the North Pacific Gyre. The Atlantic generally has really low levels of phosphorus, measurably lower than the North Pacific Gyre.

the element phosphorus among its neighbors in the Periodic Table of the Elements
the element phosphorus among its neighbors in the Periodic Table of the ElementsCourtesy modified from Wikipedia
Phosphorus is a very important element in living things. For example, it’s a necessary ingredient in ATP (adenosine tri-phosphate), the energy molecule used by all forms of life. Phosphorus is picked up from seawater by bacteria. All other marine life depends upon these bacteria, either directly or indirectly, for P. Therefore, if you’re bacteria living in the impoverished North Atlantic Gyre, you’d better be really good at getting phosphorus.

And they are!

Oceanographers at the Center for Microbial Oceanography: Research and Education (C-MORE) at the University of Hawai`i have made an important discovery. C-MORE scientists Sallie Chisholm, based at the Massachusetts Institute of Technology and her former graduate student Maureen Coleman, now a scientist at the California Institute of Technology, have been studying two species of oceanic bacteria. Prochlorococcus is an autotrophic bacterium that photosynthesizes its own food; Pelagibacter, is a heterotrophic bacterium that consumes food molecules made by others.

Pacific HOT and Atlantic BATS Stations: Microbial samples were collected at each location.
Pacific HOT and Atlantic BATS Stations: Microbial samples were collected at each location.Courtesy C-MORE
Drs. Chisholm and Coleman took samples of these two kinds of bacteria from both the Atlantic and Pacific Ocean. The Atlantic samples were collected by the Bermuda Atlantic Time-Series (BATS) program. The Pacific samples were collected in the North Pacific Gyre (about 90 miles north of Honolulu) by the Hawai`i Ocean Time-Series (HOT) program. The scientists discovered surprising differences in the genetic code of the bacteria between the two locations:

  • First of all, the Atlantic populations of both bacterial species have more phosphorus-related genes compared to their Pacific cousins. (Picture Atlantic microbes in Superman outfits with a big "P" on their chests!)
  • Secondly, in the Atlantic, Prochlorococcus has different kinds of P-related genes compared to Pelagibacter. Perhaps this means the two microbial species have evolved over time to use different phosphorus sources, to avoid competing with one another for this limited resource.

Drs. Chisholm and Coleman have discovered important micro differences between bacteria of the same species in two oceanic gyres. Now we can better understand how these microbes are working to recycle an important nutrient beneath the whitecaps.

Reference: October 11, 2010 issue of the Proceedings of the National Academy of Sciences

Apr
13
2011

Earth, our place in space
Earth, our place in spaceCourtesy NASA
Life scientists study…well, life. They want to know everything about living things on planet Earth. One of the first things biologists want to know is who’s here. What kinds of plants and animals live in a forest? --or in a field? –or in the ocean?

If you’re an oceanographer who studies marine mammals, perhaps you’d go to sea on a ship with a good pair of binoculars and hunt for whales. As you focused your binoculars you’d be able to see different kinds of whale species. As you looked closer, for example at Humpback Whales, you'd see that each individual whale has a different black-white pattern on its tail. You might even take a biopsy, a small sample of whale flesh, and do a more detailed study of genetic differences among individual Humpbacks.

But what if you’re a microbial oceanographer? You sure can't use binocs to hunt for microbes! How can you study individual differences among tiny creatures that are only one-one-hundredth the width of a human hair? How do you hunt and capture single-celled bacteria, like Prochlorococcus, the most common bacterial species in the world’s ocean?

Invent something!

laser-based micro-fluidic system
laser-based micro-fluidic systemCourtesy C-MORE
Young scientists, Sebastien Rodrigue and Rex Malmstrom, at the Center for Microbial Oceanography: Research and Education (C-MORE) were doing research in Dr. Sallie Chisholm’s C-MORE lab at the Massachusetts Institute of Technology when they adapted a “laser-based micro-fluidic system” used commonly by medical researchers, for the study of marine bacteria. With this method they could put each individual tiny Prochlorococcus cell into its own little pool of seawater.

And then the excitement began.

Prochlorococcus
ProchlorococcusCourtesy Dr. Anne Thompson, MIT
Even in scanning microscope photographs, each Prochlorococcus looks like just another teeny, tiny balloon; we can't see any individual differences. However, Sebastien and Rex used fast and inexpensive genetic methods and discovered an extraordinary variety of individual differences among Prochlorococcus. Of course the variety among these microbes doesn't have to do with tail patterns, like whales. Prochlorococcus vary in their method of getting nutrients, like iron, out of seawater.

So what? Why do we care?

We care A LOT because microbes like Prochlorococcus are operating at the nitty gritty level of cycling not only iron, but also other elements in the ocean. Like carbon. That's right, as in carbon dioxide accumulating in our atmosphere -- and ocean -- causing climate change and associated problems. The more we understand about individual differences among oceanic microbes, the more we'll understand how they influence and respond to changes in Earth's climate.

Feb
25
2011

Archaeopteryx: Thermopolis specimen.
Archaeopteryx: Thermopolis specimen.Courtesy Mark Ryan
This year marks the 150th anniversary of the announced discovery of the first fossils of Archaeopteryx, a remarkable chimera of both bird and reptile traits. The first evidence identified was a single feather discovered at a limestone quarry in Solnhofen, Germany. This was in 1860. The German paleontologist Hermann von Meyer described the fossil in 1861, naming it Archaeopteryx lithographica. That same year, the first skeletal remains came to light, and although headless, the London specimen, as it became known, showed clearly both avian and reptilian characteristics.

The unique and iconic fossil appeared just two years after publication of Charles Darwin’s On the Origin of Species and helped bolster the naturalist’s theory of evolution through natural selection because its appeared to be a transitional fossil between reptile (dinosaur) and bird. Could Darwin have asked for any better evidence?

Since then nine other specimens have been found, including the Berlin specimen around 1877, which is considered one of most complete. For many years some Archaeopteryx specimens languished in collection drawers because they had been initially misidentified as another creature entirely. In 1970, Yale paleontologist John Ostrom was investigating a so-called pteradactyl fossil at a museum in the Netherlands, when he realized it had been misidentified and was actually an Archaeopteryx. The fossil had been found at Solhofen in 1855, five years prior to the feather! The museum curator was so shaken by Ostrom’s announcement, he clumsily wrapped the specimen in a paper bag and presented it to Ostrom so he could take it back to Yale for further study. Ostrom, by the way, re-ignited the “birds are dinosaurs” debate in the 1960s after his discovery of Deinonychus and his comparison of its structural features with those of birds.

The Thermopolis specimen, the latest Archaeopteryx fossil, became known around 2005 and was donated anonymously to the Wyoming Dinosaur Center in Thermopolis, Wyoming. I happened to visit the museum in June of 2007 during the first week the fossil went on public display, and was able to see the spectacular specimen firsthand. The small fossil (about 1.5 feet square) was displayed behind a small, glass opening in the wall. There was no crowd to speak of so I was able to take in and photograph the fossil for a long stretch of time by myself. Looking at it, your eye is immediately drawn to the distinct feather impressions evident on both its wings and tail. The head, arms, and legs are spread out across the slab, and even though it died 150 million years ago, it looks as flat and fresh as road kill on a modern highway.

About the size of a large crow, Archaeopteryx was an odd amalgam of both bird and reptile. It had slightly asymmetrical flight feathers, wings, and a furcula (wishbone) - all traits found in birds. But its pelvis, skull and sharp teeth were reptilian (although some skull features are bird-like), and it ha a long tail like a reptile. Its bones weren’t hollow, like the bones of modern birds are, nor is its sternum (breastbone) very pronounced; it’s flatter and without a large keel where, in birds, muscles flight are attached. And it also possesses gastralia (“belly ribs”), a feature found in reptiles and dinosaurs. The inner toe (the hallux) in the Thermopolis specimen doesn’t appear to be reversed so it couldn't grasp or perch and was probably more earth-bound than arboreal. Interestingly, its second toe was extensible – meaning it could be pulled back and elevated for tearing into flesh, just like the middle toes of such dinosaurs as Troodon and Velociraptor. Truth be told, if its feathers hadn’t been preserved, Archaeopteryx would have been classified a carnivorous bipedal dinosaur. In fact, one of the existing Archaeopteryx fossil was first identified as a Compsognathus until preparation revealed its feathers.

Solnhofen and much of Europe in the Late Jurassic: A cluster of islands off the coast of the North American continent.
Solnhofen and much of Europe in the Late Jurassic: A cluster of islands off the coast of the North American continent.Courtesy Ron Blakey, NAU Geology
So what kind of environment did Archaeopteryx live in, and why are its fossils so well preserved? Well, during the Late Jurassic, southern Germany and much of the rest of Europe were pretty much a group of large islands poking out of the Tethys Sea off the coast of North America. What is today the Solnhofen quarry was then part of an island lagoon protected by a barrier reef. Geological evidence in the strata suggests the lagoon dried up several times followed by periods of re-flooding with seawater. Mixed into a brackish soup of coral debris and mud, and in a warm climate conducive to rapid evaporation, the lagoon’s bottom water levels became anoxic, that is depleted of oxygen. Low oxygen meant less bacterial activity and subsequently slow decomposition of any organism that happened to die or get swept into the stagnant lagoon. Burial in the carbonate muck was swift, leaving fresh carcasses no time to be pulled apart by currents or scavengers.

Solnhofen limestone has been used for centuries as a building stone. Because the rock’s matrix is so fine and splits so evenly (sediment deposition likely occurred in very calm waters), the material was later quarried to produce stones for lithography, a printing technique first developed in 1796, and the source of Archaeoperyx’s species designation. Many early scientific illustrations, including some of the first images ofArchaeopteryx were preserved as lithographs created using Solnhofen limestone.

Archaeopteryx commorative coin: Germany will issue the 10 Euro coin in the summer of 2011
Archaeopteryx commorative coin: Germany will issue the 10 Euro coin in the summer of 2011Courtesy Federal Republic of Germany
Solnhofen’s fossil record shows that the lagoon’s biological population was diverse. Fish, turtles, lizards and insects, crocodiles, crustaceans, ammonites, squid and starfish, mollusks, pterosaurs, and even the soft remains of jellyfish are preserved in the fine-grained limestone. But the premiere creature is of course the Archaeopteryx, which remains the earliest bird (or most bird-like dinosaur, if you will) known to date. As research on existing specimens continues and new fossils appear it's exciting to imagine what advances will take place in the dinosaur-bird connection debate. Whatever happens, Archaeopteryx lithographica will remain one of the most significant and iconic fossils ever discovered. It's no wonder that later this year on August 11th, the Federal Republic of Germany will issue a 10 Euro silver coin to commemorate the 150th anniversary of the discovery of its most famous fossil.

SOURCES and LINKS

Witmer Lab Archaeopteryx blog
UCMP Archaeopteryx page
Solnhofen limestone of the Jurassic

Feb
09
2011

Polyommatus blue butterfly
Polyommatus blue butterflyCourtesy Rongem Boyo
One of my favorite 20th century writers is the Russian-born Vladimir Nabokov (1899-1977). Many people were (and many probably still are) shocked by the subject of his best-known novel, Lolita, which he wrote in English in the early 1950s. But Nabokov’s use of the language in that book - and others - is at times so exquisite and so finely-crafted, that it’s equally shocking to realize that English wasn’t his native tongue but rather his second language taught to him by his governess while he was growing up in St. Petersburg. He was also well versed in French, so language played an important role in his life, as his many novels, poems, and essays attest. But growing up to become one of the 20th century’s greatest writers was not something he planned, because at age seven he had discovered another passion: collecting butterflies.

Nabokov said in later interviews that had it not been for the 1917 Russian Revolution, he would have probably been a lepidopterist at some obscure museum in St. Petersburg. But fate brought him eventually to the United States where (before publication of Lolita made him independently wealthy) he made his living mainly by teaching literature at Wellesley College and Cornell University. He also volunteered at the American Museum of Natural History - where he learned to dissect butterflies - and at the Harvard Museum of Comparative Zoology.

During the summer months he liked to mix his passions as he explained in the afterword to later editions of Lolita:

Every summer my wife and I go butterfly hunting. The specimens are deposited at scientific institution, such as the Museum of Comparative Zoology at Harvard or the Cornell University collections. The locality labels pinned under these butterflies will be a boon to some twenty-first-century scholar with a taste for recondite biography. It was at such of our headquarters as Telluride, Colorado; Afton, Wyoming,; Portal, Arizona, and Ashland, Oregon that Lolita was energetically resumed or on cloudy days.

Around 1945 he came up with a new theory of migration for the Polyommatus blue butterflies. Without the use of genetics and by studying anatomical features (mostly genitalia), Nabokov speculated that Polyommatus blues found in South America evolved by migrating in five waves from Asia across the Bering Strait. At the time the prevailing migration theories involved land bridges across the Pacific, so no one gave Nabokov’s hypothesis much weight.

Professional lepidopterists weren’t that impressed with Nabokov. They admitted he was decent enough researcher and at describing specimens (his published descriptions numbered in the hundreds) but they didn’t think he offered much in the way new ideas.

But now it seems Nabokov has been vindicated. A new report in the journal Proceedings of the Royal Society of London has determined - through DNA analysis – that Polyommatus blues have indeed evolved through five separate migrations from Asia over the Bering Strait.

“It’s really quite a marvel,” said co-author Naomi Pierce of Harvard. Pierce was part of a team of lepidopterists from England and the United States that made several expeditions to Chile to study and collect specimens of Polyommatus blues, then returned to the lab for gene sequencing and computer analysis of the data. The results showed that the Polyommatus blues did indeed originate in Asia, and were more closely related to that 10 million year-old ancestor than they were to their South American neighbors. But they also revealed that the first wave arrived when the temperature along the Bering Strait was warmer. But that temperature was in decline, and subsequent migrations brought in hardier species of Polyommatus, better suited to colder temperatures that correlated with the temperature range existing around the Bering Strait at the time of each wave. The conclusions matched Nabokov’s hypothesis to a “t”.

“By God, he got every one right,” Dr. Pierce said. “I couldn’t get over it — I was blown away.”

Paleontologist Stephen J. Gould included an essay in one of his many books about Nabokov’s split loyalties between art and science (he termed it “intellectual promiscuity”) proposing if the writer had kept focused on just writing he might have created another Lolita. On the other hand, Gould mused, if Nabokov had only studied butterflies, he could have become a well-known (at least in some obscure circles) lepidopterist. If it sounds like the old adage “you can’t serve two masters”, Nabokov seems to have pulled it off equally well in both arenas. I think had it not been for his writing and the lifestyle it afforded him, he wouldn’t have had the luxury of pursuing lepidoptery as fervently and successfully as he did; and without his butterfly collecting, he never would have written his masterpiece. If you asked the seven year-old Vladimir what he wanted most to be remembered for, his answer wouldn’t have been “writing a great novel”. He had another aspiration in mind, which he fulfilled several years later during one of his summer breaks from teaching. While visiting the Grand Canyon with his wife, Nabokov discovered a new species of butterfly which he named Neonympha dorothea in honor of a family friend who was traveling with them. His satisfaction poured out a couple years later in a poem:

I found it and I named it, being versed
in taxonomic Latin; thus became
godfather to an insect and its first
describer – and I want no other fame.

- On Discovering a Butterfly (1943) by Vladimir Nabokov.

SOURCES
NYT story
Bioephemera article

Jan
21
2011

Here's a story from the New York Times about a dog named Chaser that knows the names for more than a thousand items and even, according to her trainer, can perform more sophisticated linguistic feats such as understanding verbs and knowing that words might name a type of thing rather than an individual object.

Now, a dog that really, truly understood what you said to it would be a lot of fun to have around. (Of course, I'd probably have to curb my tendency to give dogs affectionate nicknames like Meathead and Stinky.) But even if critters like Chaser are "simply reading cues unconsciously given" by their trainers, isn't that a pretty amazing feat by itself? It seems to me that the ability to read little signals from humans, even ones that the humans aren't aware they're giving, isn't "simple" at all.

I once read a book by an animal scientist How many words does your dog know?
How many words does your dog know?Courtesy ~~Yuna~~
that said that all animals are geniuses at the skills they use to survive. Maybe Chaser really is doing something similar to what human babies do as they learn to speak and understand language. But if she's not, I'd be willing to bet that whatever skill she's using is no less fascinating.