12
April
2007
Teaching resources (UK US) designed specifically for this story at Real Science
Previous dinosaur story and teaching resources (UK US) in the Real Science archives.
The story
Scientists have sequenced tiny pieces of protein from a 68 million-year-old Tyrannosaurus rex. The fragments seem to closely match those found in today’s chickens. This supports a recent theory that birds are descended from dinosaurs.
Scientists at Harvard Medical School, Beth Israel Deaconess Medical Center and North Carolina State University did the research. They report it in the April 13 issue of Science.
It is widely believed that birds evolved from dinosaurs, said John Asara. He is director of the mass spectrometer facility at Beth Israel Deaconess Medical School. “But that’s all based on the architecture of the bones.”
Asara sequenced the protein fragments – seven of them – over the course of a year and a half. His team used sensitive mass spectrometry methods. “This allows you to get the chance to say, ‘Wait, they really are related because their sequences are related.’”
The researchers did not get enough sequences to definitely say that, he added. “But what sequences we got support that idea.”
In another study in the same issue of Science, researchers report that extracts of T. rex bone reacted with antibodies to chicken collagen. This further suggests the presence of birdlike protein in the dinosaur bones.
This work was done by Mary Schweitzer and colleagues at North Carolina State University.
The mere existence of such ancient protein contradicts a long-held belief. When an animal dies, protein begins to degrade immediately. It is slowly replaced by mineral when fossils form.
This process was thought to be complete in one million years.
For centuries it has been believed that fossilisation destroyed any original material, said Schweitzer. She is also at the North Carolina Museum of Natural Sciences and is a co-author on the Asara study.
“Consequently no one looked carefully at really old bones.”
That may now change, said Lewis Cantley. He is HMS professor of Systems Biology and BIDMC chief of Signal Transduction. He also took part in the study.
“Basically, this is the breakthrough that says it’s possible to get sequences beyond one million years. At 68 million years, it’s still possible to get sequences.”
In addition to the seven dinosaur sequences, Asara and colleagues isolated and sequenced more than 70 protein fragments from a mastodon. This was 160,000-600,000 years old. That provides further evidence of the staying power of ancient protein.
There are important implications for handling newly discovered fossils, Asara said. Even with really old fossils people should avoid contamination. They should also “ensure that whatever is there gets well preserved because it can be interrogated.”
The scraps of dinosaur protein were obtained from a T Rex fossil femur. This had been discovered by John Horner, of the Museum of the Rockies, and colleagues in 2003. The location was Hell Creek Formation, a barren fossil-rich stretch of land that spans several states.
The scientists faced two challenges. The first was to gather enough protein to sequence. The bone extract was in the form of a gritty brown powder that had to be rid of contaminants. Asara purified the protein – identified as collagen – and broke it down into fragments, 10 to 20 amino acids long. He used techniques developed while working on the mastodon sample.
The peptides were passed over a liquid chromatography (LC) column. This separated them from one another. They were then sprayed at extremely low flow rates, for best sensitivity, into a mass spectrometer.
This measures the mass – specifically the mass-to-charge ratio – of peptides as they come off the LC column. To get the greatest possible yield, Asara used an ion-trap mass spectrometer. This captures and holds peptides.
The collected peptides were measured for mass. In a second step, they were isolated and fragmented to reveal their amino acid sequence. Using this two-step procedure, Asara gained seven separate strings of amino acid.
He now faced his second challenge. This was to make sense of the amino acid sequences. Normally, when a sequence comes out of a mass spectrometer, it is compared to a database of existing amino acid sequences. Collagen is a protein that does not vary much with evolution.
So it was highly likely that some of the dinosaur peptide sequences would match those of an existing species. Of the seven T. rex peptides, five were for a particular class of collagen protein – collagen alpha I. These were found to be matches to amino acid sequences in chicken collagen alpha I.
For extinct species, the real goal is to find sequences unique to that organism. Asara generated a set of theoretical collagen protein sequences. These were some of the kinds that might have been present around the time of T. rex.
None of his dinosaur peptides matched the theoretical set. But this is not surprising. “If you’re only finding seven sequences in T. rex, you’re not going to find novel ones,” said Asara.
He also tested mastodon bone, sent by Schweitzer, against a database of existing amino acid sequences and against mastodon theoretical sequences. He identified a total of 78 peptides, including four that were unique.
The team will get better at doing the extractions, Cantley said. And their instruments and techniques will improve. That means they will be able to get “much more extensive sequences” from ancient fossils. They should also get “novel sequences unique to that species, which will give us ideas about the relationship between species.”
Still, it may be very rare fossils that are as well preserved as the T. rex and mastodon specimens analysed in the current study.
“Nature has to give you the opportunity to do this first,” Asara said.
Links to free teaching resources for this story
Proteins are about half the dry weight of most cells, and are the most complex macromolecules known. Each protein has a unique structure and function. Includes nice amino acids interactive.
Narrated animation of protein synthesis, starting with DNA, which is transcribed into messenger RNA, which leaves the nucleus and binds to a ribosome. Transfer RNAs then attach and build a polypeptide chain that folds into a protein.
Learn how modern scientists can use a tool not available in Darwin’s time: molecular evidence. Molecular biologists have uncovered genetic links between diverse animal species, providing new evidence of common ancestry.
Companion website to the NOVA program Curse of T. Rex, which follows the trail of legal and illegal fossil-dealing as the FBI tries to protect the best Tyrannosaurus rex specimen ever found from winding up on the shelves of a souvenir shop.
When dinosaurs ruled the Earth from Discovery School. Students will understand: The age of the dinosaurs is called the Mesozoic age. It is divided into three periods, the Triassic, the Jurassic and the Cretaceous. Plants and animals on Earth differed during these three periods…
“Building a free-standing mount of a forty-foot skeleton wasn’t easy.”
“The more we learn about dinosaurs the more fascinating they become. But how do we know they really existed? And how do we know so precisely when they lived? The fossilised dinosaur bones and tracks in this still collage produced for Teachers’ Domain offer physical evidence – the foundation of all science – of the dinosaurs’ existence.”
Lesson from a teacher designed to give students a different way of looking at genetics and biotechnology. “After reading the novel “Jurassic Park” by Michael Crichton, I decided to incorporate the ideas of the novel into my genetics unit. Crichton is a graduate of Harvard Medical School and does an exceptional job of blending science and suspense; a perfect blend for any high school science student.”
Dinosaur Detectives from Discovery School. Students will: Understand that discoveries about dinosaurs have a long history and that each palaeontologist adds his or her work to a body of fossil evidence used to support theories about dinosaurs. Find out that palaeontologists often support one theory over another until additional fossil evidence …”
“The study of dinosaurs stretches our imaginations, gives us new perspectives on time and space, and invites us to discover worlds very different from our modern Earth.” Questions and answers from US Geological Survey.
Links to more links
Archaeopteryx, ancient birds, and dinosaur-bird relationships.
Lesson plans and activities for teachers based on DNA series from PBS.
Posted: Biology
28
March
2007
Links to free teaching resources for the story on ballooning spiders
Teaching resources (UK US) designed specifically for this story at www.realscience.org.uk
“Meet a jumping spider named after the character Portia in Shakespeare’s The Merchant of Venice, for her habit of deceiving her enemies. Another jumping spider demonstrates an affinity for watching TV, much to the surprise of arachnologists studying her behavior. Scientist Dave Clark suspects he could be seeing the first stage of an evolving spider species.”
When Gondwana broke up, spiders were isolated on separate continents, where they evolved independently… Spider species are often good travellers. Many of these spiders get around by behaviour called ballooning. “Young spiders, and even small adults of some species, put out silk threads which are caught by the wind, carrying them up and away.”
“Researchers have developed a new model that explains how spiders fly into new territory on single strands of silk – sometimes covering distances of hundreds of miles over open ocean.” Earlier news story on how the Rothamsted scientists developed their ballooning model.
“As you see in this episode, arachnophobia can be treated using virtual reality therapy.” SpiderWorld with virtual spiders.
Lovely series of lessons on spiders for K-3, which pulls together science, math and language. English and Spanish.
Some tiny insects and spiders drift through the sky in the same way that plankton drifts in an ocean. These tiny bugs floating through the air are called “aeroplankton” or “aerial plankton.”
How in the world did spiders get to Hawaii? They floated on air currents! One of the most popular spiders in the world, the Happy Face Spider
“Would you like to adopt a Hawaiian Happyface Spider? These tiny spiders were discovered in 1973 in the rainforests of Hawaii.”
Nice collection of ballooning and Charlotte’s Web activities. “Baby spiders have no wings, but can fly as high as the highest-flying insects and birds! In fact, ballooning spiders often hit airplane windshields. How can a spider, with no wings, possibly get this high in the air? You’ll find out by reading this week’s report and helpful links that follow.”
Links to more
Acorn Naturalists, resources for the trail and classroom.
Spiders and their relatives.
The story:
Soaring spiders
Spiders ride the wind on silken threads. It is called ballooning. They do it to carry themselves out of danger or into new territory. And in the right conditions they can sometimes fly through the air for hundreds of miles.
But nobody knew until now why ballooning reaches a peak in spring and autumn, and is much less common in windy and sunny weather. Sunshine after all produces more updrafts, which are helpful for take-off.
Now a team at Rothamsted Research has developed a model of ballooning. This shows that light breezes and moderately warm weather are the best spider ballooning conditions. This is typical weather for spring and autumn.
These results could lead to a non-chemical alternative to pesticides for managing crops.
The team of biologists and mathematicians used the model to investigate travelling distances under a range of conditions of wind and sun. They were aiming to find the best weather for flight.
Hot days do indeed produce more updrafts. But the wind is not usually strong enough to carry the spiders very far, the scientists found.
On the other hand, if the wind becomes too strong the updraughts are disrupted, the model shows. This makes flight impossible.
Spiders hunt and eat pests like mites and aphids. So predicting spider ballooning peaks is important for crop management.
In the growing season, around 1800 spiders a day land in each hectare of arable farmland after ballooning, explains Dr Andy Reynolds of Rothamsted Research. “If the farmers can predict the influx of spiders, they can reduce the amount of pesticides accordingly.”
The research team is planning field experiments to test the model. This could provide valuable information on other organisms that use the wind for transport. These include mites and viruses.
This research is a good example of interdisciplinary collaboration, said Professor Julia Goodfellow. She is chief executive of the Biotechnology and Biological Sciences Research Council. “Biologists and mathematicians together have produced new knowledge which can help lead to environment-friendly pest control.”
Rothamsted Research is in Hertfordshire, England. It is a sponsored institute of the Biotechnology and Biological Sciences Research Council (BBSRC).
Posted: Biology
14
March
2007
Links to free teaching resources for the science story below:
Teaching resources (UK US) designed specifically for this story at www.realscience.org.uk
Set of lessons on gene inheritance: Students learn how genes are passed from one generation to the next. They explore meiosis, which divides the genetic material of an individual in half to produce the sperm or egg cells. They explore how genetic diseases are passed from one generation to the next. A coin-toss exercise demonstrates the odds of parents passing mutated genes to their offspring. Two videos illustrate positive, negative and neutral effects of mutations. From Teachers’ Domain. Simple registration required.
“A mysterious biological mechanism that subtly changes the way people’s genes behave may account for many of the surprising differences between identical twins…” Washington Post. Background on epigenetics.
“Recent revisions to the basic mechanisms of modern genetics violate many long held ideas of inheritance.” Teacher background, since “older textbooks will not have references for these genetic surprises.”
“If you thought that DNA has no secrets left to surrender, think again. The sequencing of the human genome may have heralded a new era for genetic research, but the unravelling DNA story still has a twist in its tail. The new buzzword in many corners of the establishment is epigenetics…”
“How does the environment alter the phenotype? Identical twins are not interesting merely because they are different: everybody’s different. Instead, they are interesting because they show how the same genome can unfold differently with slightly different conditions.” Prominent scientist weblog touching on epigenetics.
“The only important thing about DNA is its sequence, right? Wrong.” Teacher background on epigenetics and methylation.
Activities and instruction on how memory works, and on Alzheimer’s disease. From PBS.
Activity page on memory, with: a minds-on and hands-on experience; an opportunity to compare memory tricks; tools and ideas for improving memory.
The story:
University of Alabama: 14-Mar-2007, 12:00 Eastern US Time, Eurekalert.
Memories are made of this
Scientists have discovered a mechanism by which the constantly changing brain makes its memories—from a dog-bite to that first kiss.
It’s the same mechanism that cells use to alter their genes during development of the embryo.
Neurobiologists Courtney Miller and David Sweatt report their findings in the March 15, 2007 issue of the journal Neuron.
Their studies were aimed at exploring if a process called DNA methylation plays a role in making memories.
In methylation, molecules called methyl groups are attached to genes. This switches them off. Cells use methylation when the embryo is developing to switch off particular genes. This lets the cells specialize into different types – skin, bones, hair, etc – as the embryo grows and develops.
The name for this process is “epigenetic”. Epi means “above” or “in addition”. So epigenetic means that something is happening in addition to the normal action of the genes.
During development of the embryo, methylation causes a permanent change in the activity of genes. Previous studies had hinted that methylation stays active into the adult brain. But it wasn’t thought to be a mechanism for making long-term memories.
On the other hand, mistakes in DNA methylation are seen in some brain disorders, such as schizophrenia.
So Miller and Sweatt designed experiments to test if methylation helps make memories. In their experiments they produced fearful memories in rats. They gave the animals mild shocks when they were in a particular training chamber.
They could then test if the rats remembered, by noticing if they froze when placed in that chamber.
Then they gave the animals drugs that inhibit methylation. This was to test if methylation was needed for the rats to form these memories.
The researchers found that it was. They also found that methylation directly controls the activity of two genes. One of these prevents memories being formed. It is called protein phosphatase 1. The other helps memories form. It is called reelin.
DNA methylation was once thought to be a static process after cell differentiation – when cells had become part of the different organs of the body. This study is the first to find evidence, say the scientists, that instead it is “dynamically regulated in the adult nervous system”, and “plays an integral role in memory formation.”
The new findings show that DNA methylation is used by the central nervous system. This is a key step in controlling gene activity to make memories.
In terms of possible applications of the work, epigenetic errors have been seen in cancer, some types of autism and schizophrenia. So the new findings could improve our understanding of the causes of those disorders.
More broadly, the findings show the importance of DNA methylation in changes in the brain caused by events in the environment
###
The researchers include Courtney A. Miller and J. David Sweatt of University of Alabama at Birmingham in Birmingham, AL.
This work was supported by the NIMH, NINDS, American Health Assistance Foundation, and the Evelyn F. McKnight Brain Research Foundation. C.A.M. is a Civitan Emerging Scholar.
Miller et al.: “Covalent Modification of DNA Regulates Memory Formation.” Publishing in Neuron 53, 857–869, March 15, 2007. DOI 10.1016/j.neuron.2007.02.022. www.neuron.org.
Posted: Biology, Chemistry
22
February
2007
Topics for group discussion, pupil presentations or blogging.
A great way to get young people talking about science is through blogging. There’s a blog on just about every topic you can imagine. A good safe place to start looking for schools active in blogging is Scotedublogs
This has a listing down the left-hand panel of school blogs grouped by local authority. Notice that Shropshire, despite what it says, is definitely not in Scotland. It’s like-minded teachers they want, not schools in particular locations.
There is not a lot on science there yet. But take a look at Commentsforkidz and get blogging with colleagues and pupils in schools around the world!
Links to free activities, resources and lesson plans
Teaching resources (UK US) designed specifically for this story at www.realscience.org.uk
To help students understand animal intelligence, have teams design an experiment in which they test a question related to animal behaviour. Work through one of the following: Do goldfish respond to music? Do dogs remember what happened a day earlier? Can cats plan for a future event?
Almost everything scientists thought they knew about bird brains being primitive and instinctive has been found to be wrong. Fully 75 % of the brains of parrots, hummingbirds etc. is a sophisticated information processing system that works much the same way as the cerebral cortex in humans. Take a look at a rotating model of a songbird’s brain. From Nova.
Meet scientist Erich Jarvis and hear why he finds bird brains so interesting.
Question and answer session with a bird-brain expert.
Some abilities are supposed to be unique to humans. The trouble is they keep turning up in animals too.
Have you ever wondered what makes humans different from rats, or wanted to see a cerebellum? Have you ever looked at a frog and wondered if it has a cortex? Do you want to know how intelligence is defined? From Serendip.
“Birds may have a reputation for being less than geniuses, but researchers are discovering that some are remarkably smart.” With links to interactives and learning games on animal emotions and social awareness. From PBS.
Lots of examples of bird intelligence.
Links to more links
Several of Prof Nicky Clayton’s papers on scrub jay intelligence in pdf form.
Links to lots of bird lessons and activities. From AOL.
Posted: Biology
17
February
2007
In the bayous of Arkansas a high-tech sentinel patiently waits to capture an elusive bird… more
Links to free activities, resources and lessons
Teaching resources (UK US) prepared specifically for this story from www.realscience.org.uk
“Tell students that they have just been hired as photojournalists for Backyard Jungle News. Their assignment is to find the most exciting news taking place in their backyard today. Explain to students that they will have to convince the editor that their story and image should be front page news. Relate the story of the ivory-billed woodpecker: ‘Only one hundred years ago …’” From Backyard Jungle.
Cornell Lab of Ornithology website, with video clips, photos, sounds and ‘meet the search team’.
Lovely, full-colour brochure (pdf) on the ivory-billed woodpecker. From US Fish and Wildlife Service.
Another project using different technology to hunt for the famous woodpecker. From NASA.
The Search for the Ivory-Billed Woodpecker. “More than 60 years after the ivory-billed woodpecker was thought to be extinct in the United States, researchers now have found evidence that the majestic bird may still live …” From The Nature Conservancy.
Listen to Phillip Hoose, author of The Race to Save the Lord God Bird, speak about the recent rediscovery of the ivory-billed woodpecker in a live online audio chat
Timeline of the Ivory-Bill Search. Includes Luneau’s disputed video of the bird. Needs broadband.
“These Ivory-billed Woodpecker calls were recorded at close range in 1935 by Arthur Allen and collaborators in the Singer Tract, Louisiana. The clip here was extracted from about five minutes of recordings at a nest cavity where both male and female were present.
“Listen to calls recorded near a pair of Ivory-billed Woodpeckers at a nest cavity using Interactive Analyzer or Simple Sounds. Choose Interactive Analyzer to explore the sonogram and see it scroll across the page as the sound plays. Choose Simple Sounds for a faster download of a fixed sonogram and an audio file.” From Cornell Lab of Ornithology.
“In more than 17,000 hours of recordings, thousands of double-knock sounds were detected. After eliminating noises made by raindrops, gunshots, and other sources, researchers at the Cornell Lab of Ornithology found about 100 double knocks that sound tantalisingly similar to …”
US fish and wildlife service. “Ivory-billed woodpecker recovery starts here.” From US Fish and Wildlife Service.
Ivory-billed woodpecker FAQ (pdf), including what to do if you see one.
Send an ivory-billed woodpecker e-card.
BACK to original story at www.realscience.org.uk
Posted: Biology
9
February
2007
BACK to the website at www.realscience.org.uk
The links below were all going to one website yesterday – Science NetLinks.
Nice site, but not quite what I intended. It’s all fixed now.
Links to free activities, lesson plans, and background information
http://www.sciencenetlinks.com/lessons.cfm?BenchmarkID=11&DocID=210 To make models of insects, and to use the Internet for insect exploration. “Models are tools for learning about the things they are meant to resemble. Physical models are by far the most obvious to young children. (Science for All Americans, p. 4.) During the process, you can help students think critically about the differences and likenesses between actual insects and models… students should begin to have a better understanding of the usefulness of models in general.” From Science Netlinks
http://www.teachersdomain.org/resources/eng06/sci/engin/systems/robofly/index.html Plant and animal species survive by adapting to different challenges. So scientists are now looking to nature for help with engineering challenges. In this video segment from NOVA, engineers study insect flight to gain insights into design of miniature flying vehicles. Teachers’ Domain. Simple registration required.
http://www.educationworld.com/a_lesson/lesson/lesson192.shtml Do your students know the real difference between a fly and a mosquito, an insect and a spider, a true bug and a bedbug?” Classroom activities from Education World.
http://www.teachersdomain.org/resources/eng06/sci/engin/systems/futurefly/index.html The Wright Brothers found inspiration for their first airplane in a bird’s flexible wing. The craft was steered by pulleys and cables that twisted the wingtips. In this video segment adapted from NASA, learn how nature has inspired aerospace engineers to design the next-generation of flying machines.
http://www.teachersdomain.org/resources/phy03/sci/engin/design/uavs/index.html Interactive timeline from NOVA, which charts the evolution of unmanned aerial vehicles (UAVs), from the earliest bomb-dropping balloons and kites with cameras, to sophisticated stealth craft the size of your hand.
http://members.aol.com/YESedu/kidsfun.html Insects have been described as “the little creatures that run the world”. Activities for different age groups.
http://www.laps.univ-mrs.fr/~ruffier/anglais.html Researcher’s homepage with links.
Links to more
http://www.urbanext.uiuc.edu/insects_sp/guide/activities.html Insect experiments for the junior school.
http://www.theness.com/articles.asp?id=41 Chat about the myth that scientists proved bumble bees can’t fly.
http://www.news.cornell.edu/chronicle/00/3.30.00/insect_flight.html Computer simulation of moving wings and fluid flow has proved that aerodynamics applies to insect flight.
http://www.news.cornell.edu/releases/March00/APS_Wang.hrs.html
“Looking ahead to the construction of tiny flying machines for aerial surveillance and other purposes, Wang says the designs need not resemble fixed-wing airplanes or helicopters.”
BACK to the website at www.realscience.org.uk
Posted: Biology
3
February
2007
It occurs to me that links to additional online resources are not particularly useful inside a Word document – which is where I’ve been putting them.
So from today I’m going to take this section out of the Word document and place it here, where you’re just a click away from taking a look for yourself.
Links to free activities, lesson plans and background information
http://www.actionbioscience.org/education/guilfoile.html
“The purpose of this article is to help teachers integrate biotechnology into their classroom, by providing resources along with background information and a guide to appropriate topics and exercises.”
http://www.norfolkcoast.co.uk/location_norfolk/vp_stiffkey.htm
http://www.northnorfolkimages.co.uk/location/stiffkey.html
All about Stiffkey – which is pronounced ‘Stewkey’. “Contrast the purple carpet of Sea Lavender (Limonium vulgare) and the aromatic, grey-green Sea Wormwood (Artemesia maritima). …While all around is the perpetual sound of its birdlife.” And watch out for the ghosts….
http://learn.genetics.utah.edu/units/activities/print-and-go/dnaextract.cfm
Students extract DNA from the pea (Mendel’s organism of choice) using common household chemicals. This basic protocol can be used to extract DNA from other sources too, demonstrating that the DNA molecule is present in all living things.
http://www.soc.soton.ac.uk/gg/classroom@sea/general_science/food_webs.html
Plankton and marine food webs: “All organisms in an ecosystem are linked together by their feeding relationship. The sequence of steps that represent the feeding relationships are the food chains.” http://www.ifgene.org/glossary.htm Glossary of genetics and genetic engineering with key to abbreviations
http://library.thinkquest.org/C003763/index.php?page=planet06
Background on Gaia hypothesis of James Lovelock and Lynn Margulis. This states that the interactions of all the organisms and all the environments of Earth make it a single organism. There is a link to an animation of Daisyworld, which illustrates the idea in an appealing way.
http://school.discovery.com/schooladventures/planetocean/tips.html
Planet ocean project from Discovery School: “While not as endless as the universe, the ocean is huge. As a teacher you can approach studying the ocean in different ways: Explore the geological processes at play. Discuss the different environments within the ocean. Go back in geological time and talk about how life evolved in the ocean.
http://www.education-world.com/a_lesson/lesson060.shtml
Eighteen activities for students to practice their math, geography, science, and language skills while learning about the world’s oceans.
http://www.teachersdomain.org/resources/tdc02/sci/life/gen/moleclevgen/index.html
Think all DNA resides in the nucleus? Want to know how to decipher a DNA code into protein? This article, filled with colourful visuals, goes down to the microscopic level as it explains the workings of DNA, RNA and proteins inside living cells.
http://en.wikipedia.org/wiki/Dimethyl_sulfide
Brief background on dimethyl sulphide and its importance.
http://saga.pmel.noaa.gov/review/dms_climate.html
Teacher background on dimethyl sulphide.
Links to more links
http://seawifs.gsfc.nasa.gov/OCEAN_PLANET/HTML/search_educational_materials.html
Educational materials from the Ocean Planet exhibition by the Smithsonian Institution.
http://gila.lib.utk.edu/mediacenter/revolution/3-resources.html
More genetics, including links to biotechnology websites.
BACK to the story at realscience.org.uk
Posted: Biology
