Ibex: Capra ibex
Courtesy Nino BarbieriA recent article in the Journal of Archaeological Science reminded me of the importance of the Scientific Method Often we hear new and exciting scientific theories that seem plausible, especially if these ideas are presented in prestigious journals. However, the beauty of the Scientific Method is its verifiability, whether or not the data can be recreated through repetitive testing (If we truly believed everything the first time, our budding young scientists would have nothing to do!)
Michael Campana from the University of Cambridge and colleagues from across the UK and Ireland recently ran a sequence of DNA tests on 18th and 19th century parchments made from animal skins in order to reveal the complexities of ancient parchment analysis. Parchment is one of the most valuable archaeological and historical artifacts that can be used to understand not only language and history, but DNA testing on it can reveal clues to animal population studies, animal husbandry, different historical animal breeds, and provenance (where the animal or skins originated from). In the case of the Dead Sea Scrolls, DNA testing on the parchment could reveal what type of animal was used and possibly where it came from, providing additional data for questions regarding who wrote the scrolls.
Campana and colleagues analyzed both mitochondrial and autosomal genetic data using stable isotope, genetic, phylogenetic and ion beam analysis. All samples were considered to be well preserved and ideal samples for accurate testing. All but one parchment produced multiple DNA sequences that matched several different species including cow, goat, sheep, and even human. In other words, a parchment assumed to be made from one individual of one species, gave conflicting results as more than one species or more than one individual. Of course it can be assumed the parchment was not made of human skin and therefore human genetic data must have came from handling and processing of the parchment, but parchments can also be contaminated in long-term storage or contact with each other. Testing results can also be skewed by glues and inks or other preparatory treatments used to improve the surface. All of these factors need to be considered when testing truly ancient parchment like the Dead Sea Scrolls.
Previous DNA test results from 2001 and 1996 on the Dead Sea Scrolls produced results pointing to a single species, either ibex (Capra ibex) or domestic goat. While these results may indeed be correct, the likelihood that the results were so exact, when testing such as Campana's and colleagues on better preserved and more recent parchment were so complex, questions the accuracy of the earlier DNA testing. Of course we must not forget, precious artifacts like the Dead Sea Scrolls can not be needlessly dissected to offer unlimited samples for DNA testing labs. But as, Campana states, “Improving our understanding of parchment's DNA content would allow us to develop a predictive model for sampling of historic manuscripts.”
So the messages for today, bravo for the Scientific Method and go see the Dead Sea Scrolls at the Science Museum! Learn the science, archaeology, history and more that surround these amazing artifacts. Ask questions like: did the scroll writers choose ibex for some scrolls over goat because they thought these documents were so special or was ibex as readily available as any other animal species? Did the handling of the scrolls by shepherds who supposedly found them contaminate the actual scroll DNA with sheep, human or goat DNA? What can DNA testing tell us about other ancient artifacts? As long as there are unanswered questions, no matter how small, there will be a need for scientific investigation; which is good news for our future scientists!
Tags : No, I'm not talking about the lousy cold you have, or the H1N1 flu (for which I just got a vaccine), or the seasonal flu. I'm talking about how researchers in Japan and at the University of Texas at Arlington have discovered that eight percent of the genetic make-up of humans and other mammals comes from an outside virus and not from our ancestors. After infecting a body, the viral DNA inserts itself into the body's cell nuclei (endogenization), and some of its genetic material is subsequently passed along to the host's offspring. The scientists plan to investigate whether such infections by bornavirus genes are the cause of some human psychological afflictions such as schizophrenia. The research appeared in the science journal Nature.
SOURCES
University of Texas - Arlington press release
More in the journal Nature
IBM plans to speed up DNA sequencing using tiny holes in silicon. Read about it here.
Growing computers with DNA
Scientists from California Institute of Technology and IBM have for the first time coaxed components made from DNA to self organize in a way that could serve as a template upon which additional components like wires and switches could attach.
This technique, which "grows" nano circuits rather than "tooling" them, could result in smaller circuits and save millions of dollars.
Learn more at SiliconValley.com:
IBM scientists take big step toward DNA microchips
Birch barkode?
Courtesy Mark RyanA group of international scientists are planning to barcode the DNA of all of Earth's plant-life so a library can be established that will make it easier for botanists to identify plants. A standard barcode cataloging of a plant's genetic make-up would make it easier to identify it from fragments or from premature forms such as seeds or spores. It could also aide in halting the illegal trade of both indigenous and invasive species. Dr Peter Hollingsworth, head of genetics and conservation at the Royal Botanic Garden, in Scotland and the lead author of the study, says identification is important.
"It is the link between a given plant and the accumulated information available for that species," he said. "It is not possible to know whether a plant is common or rare, poisonous or edible, being traded legally or illegally, unless it can be identified."
The findings appear in the recent issue of the Proceedings of the National Academy of Sciences. Go here to read more.
Have scientists finally found a Rock n' Roll gene? Not really, but researchers have made some interesting discoveries about the genetic basis of birdsongs, which are passed down from generation to generation through social interaction much in the same way that you or I learn to talk, sing, dance, cook or create. When the authors of a new study on the transmission of birdsong behaviors in zebra finches isolated and raised birds in silence, they expected them to sing off-key. While the mating songs of these 'untrained' birds were much less appealing to the opposite sex, after several generations the untrained lineage produced offspring that were able to sing just like those in the wild. You can listen to the experiment here. This news has left researchers wondering where birdsongs originally began, and to what extent cultural behaviors are hard wired. While zebra finches and humans are only very distant relatives, researchers think we may be able to learn about human culture and genetics from studies like these. After all, as the authors point out, our human cultures (including language, music and a whole host of other things) are very different, but they all share common elements across the globe. In the end, these cultural underpinnings may turn out to be part of our biology.
Viva la evolution! Antibodies show Darwin's theory at work
in Life Science, Cells, Heredity, Biological Populations Change Over Time, and Human Organism
Influenza virus: Negative-stained transmission electron micrograph (TEM) depicting the ultrastructural details of a number of influenza virus particles, or “virions”.
Courtesy pingnews.comEvery time flu season comes around there seems to be concern whether the current flu shot vaccine will be able to stave off the viral attack. That’s because viruses and bacteria have a habit of mutating, which subsequently makes a particular vaccine against them ineffective. So each year the medical profession comes up with a vaccine they think will be an effective counterattack against the invading virus. Our own natural antibodies do something similar.
"We've known for a long time that our antibody-forming system adapts itself to every microbe we encounter," said Gerald Weissmann, M.D. He’s Editor-in-Chief of the FASEB Journal where a new study on the subject appears. “What we didn't understand fully is exactly how this happens,” he added.
When viruses or other microbes attack us, our body’s defense system goes into action - via evolution - figuring out ways to create antibodies that will successfully neutralize the invader. There’s two ways our bodies do this: either by mutation of a single cell or mutation of a cluster of cells.
New research out of Detroit’s Wayne State University shows how clusters of our cells quickly customize themselves to fight new forms of attacks. It has to do with how our genes code for antibodies. When a RNA polymerase replicates DNA it moves across it like a scanner. If the scan is smooth, a single mutation (or none at all) takes place. But if the RNA is stalled over the DNA then in some cases multiple mutations occur. The process allows for rapid deployment of tailor-made antibodies to attack the invader.
Why is this important? Well, according Weissmann, as our climate warms the ranges of parasites and microbes expand, making more people vulnerable to infectious diseases than they have been in the past.
“Now that we know [how cluster mutations occur], we can begin to find ways to manipulate this process so illnesses can be prevented or made significantly less dangerous."
LINKS
Science Daily report
DNA from the Beginning (good primer)
Explanation of the polymerase chain reaction
Forensic Archaeologists search for evidence of genocide
Archaeologists excavate mass graves in Iraq.
Courtesy US Army Corps of Engineers, St. Louis District and Regime Crimes Liaison OfficeIt’s the last weekend to go check out the CSI exhibit which takes visitors through the process of gathering forensic evidence and solving a case and the January issue of Archaeology magazine offers a really interesting look at how forensic techniques can be used on a large scale. It follows the role of American archaeologists in gathering evidence used in the trial of Saddam Hussein and other leaders for the 1988 mass murder of Kurdish people in Iraq.
Investigators had many documents suggesting the previous Iraqi leaders were guilty of genocide and had found what looked like mass graves. However, they looked to excavating the graves and locating the bodies in order to prove that the previous Iraqi government had targeted a civilian population of a particular ethnicity.
Mobile camp to analyze remains and artifacts
Courtesy US Army Corps of Engineers, St. Louis District and the Regime Crimes Liaison OfficeA team of archaeologists from the U.S. Army Corps of Engineers surveyed the desert and found 10 burial pits all oriented in the same direction. They uncovered one of the pits and photographed it. Then they removed each body with its clothes and belongings one at a time, marking each one’s position. They made a case file for each victim and analyzed each individual’s clothing, bones, and DNA samples to reconstruct what had happened.
I was shocked to read that of the 114 people they found, 84 were children. From the belongings people had with them, the team thought that the victims expected to be relocated but were instead led into a one of 10 already dug pits and shot.
The archaeological evidence was used in court along with government documents and eyewitness accounts including the testimony of a man who had survived the massacre. Hussein had been sentenced to death in another trial, but five of the other six defendants were convicted.
The team of archaeologists stayed to excavate and return the bodies to Kurdish officials, who held a reburial ceremony and plan to use some of the objects for a holocaust museum.
Court ruling against Britain's DNA storage
DNA model
Courtesy YnseBritain’s current process of collection and storage of DNA and fingerprints faces a major upheaval. The European Court of Human Rights ruled on Thursday that storing such information was a violation of people’s privacy rights. Britain now has until March to destroy almost 1 million of the DNA samples they have stored or make a case for keeping them.
Seven years ago, a man and a teenager were arrested for two unrelated crimes and both charges were later dropped. Both requested that their DNA samples be destroyed, but police refused, keeping the samples on file. Britain previously stored DNA samples of anyone arrested even if they were not convicted of a crime. They keep the samples until the person’s death or until they are 100 years old.
Britain has over 4.5 million samples of DNA, one of the largest databases in the world. Many officials are unhappy with the court ruling, noting that the information has been valuable in solving many recent cases. Human rights groups contend that the court’s decision respects the privacy rights of innocent citizens.
The United States currently allows collection of DNA from convicted felons. However, they have announced plans to collect DNA from people arrested by federal agencies as well as foreigners who have been detained.
Do you think that storing DNA samples is a violation of privacy rights or is it necessary to solving criminal cases? What do you think are fair standards for collection and storage?
You can read more about this at European court makes landmark ruling on DNA rights
Nicolas "Sly dog" Copernicus: What's he thinking about? What's he looking at? The stars? Young research assistants? His future as a cyborg?
Courtesy Regional Museum of TurunLost for hundreds of years, the final resting place and remains of the father of modern astronomy, Nicolas Copernicus, have been found in the Frombork Cathedral in northern Poland.
Copernicus was born in 1473 in Torun, Poland, and he was the first European to suggest that the Earth rotated on its own axis once a day, and revolved around the sun once a year. Followers of the Ptolemaic theory, which had the universe revolving around the Earth, were all, “Say what?!” And some of them were even, like, “Oh no you di’n’t” and snapped in Z-formation at him. Copernicus was all “Believe it, y’all.”
But then Master C died in 1543, and seventy-three years later a pope condemned his work as contrary to scripture, and a lot of people were all “Copernicus who?” And we all forgot exactly where he was buried.
The Bishop of Frombork, however, had the notion that DJ N.C. Astronomy might be hiding out in the tombs beneath the cathedral. A few years ago, archaeologists found a body that more or less matched Copernicus’ description (male, about 70 years old, dead), but it was only recently that geneticists were actually able to confirm the identification of the remains—DNA taken from the skeleton matched DNA taken from two strands of hair found in a book known to have belonged to Copernicus.
Debate on the issue has now centered on best way to resurrect Copernicus. German researchers, for the most part, are strongly in favor of the zombie method, while their polish counterparts argue that the strength and processing power of a cyborg frame would better suit the crumbly astronomer. French scientists are dead set on cloning a younger, sexier body for Master C. The Bishop of Frombork, meanwhile, just wants to put something nice together for the tomb.
Any thoughts?
UPDATE 11/21—I just came across this article this morning. It's mostly the same information that was in the other article I linked to, but there's a cool image of the facial reconstruction from Copernicus' skull. The final image really does look like Copernicus as an old man.
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