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Wednesday, September 21, 2016

Antikythera Mechanism Shipwreck Revisited: Human Skeleton Over 2,000 Years Old Discovered at Site

      Parts of a 2,000-plus-year-old skeleton have been recovered from the shipwreck which contained an early analog computer, the Antikythera Mechanism, which we discussed here at Partial Ellipsis of the Sun in 2014.

      Researchers found the skeleton last August during their ongoing excavation of the wreck, which lies on the ocean floor off the Greek island of Antikythera in the Aegean Sea.

      “Against all odds, the bones survived over 2,000 years at the bottom of the sea, and they appear to be in fairly good condition,” Dr. Hannes Schroeder, DNA expert, of the Natural History Museum in Copenhagen, Denmark, said.

     The discovery consists of a partial skull with three teeth, arm and leg bones, and several parts of ribs as reported yesterday in Nature. They are the first bones to be recovered from the wreck, particularly exciting during this era of DNA sequencing.

       The passenger or crew member “was trapped in the ship when it went down and he or she must have been buried very rapidly or the bones would have (been) gone by now.” Some of the bones remain on the seafloor, but others have been brought to the surface for analysis.

      If the research team, which is led by experts from Woods Hole, can recover DNA from the skeleton, they may be able to confirm the individual’s gender and hair and eye color, as well as his or her ethnicity and geographic origin.

      The wreck, which is believed to be of a Greek trading or cargo ship, is the largest ancient shipwreck ever discovered. Since its discovery by sponge divers in 1900, divers have recovered extraordinary artifacts including glassware, gold jewelry,

marble statues and an ancient weapon known as a "dolphin,"

a lead and iron artifact that weighs about 220 pounds. "Dolphins" were defensive weapons that were dropped from the ship’s yard, a spar on the mast, onto the deck of an attacking ship, such as a pirate vessel. 

      The Antikythera Mechanism remains the star of the seafloor find, at least so far.

       These are the best of (DNA) times. . .

Speaking of times, we are close to the 3-year anniversary of Partial Ellipsis of the Sun on October first!


Tuesday, September 13, 2016

Speaking of Geologic Time Periods Ending in E: Indian Fossils and the Spread of Primate-Like Animals: India's Island Days

      Well-preserved bones of rat-sized creatures excavated in an Indian coal mine may come from close relatives of the first primate-like animals, Iowa, USA, researchers describe.

     A set of two dozen limb fossils, dating to about 54.5 million years ago during the Eocene, raises India’s profile as a possible hotbed of early primate evolution, says biologist Dr. Rachel Dunn. 

      Bones from Vastan coal mine in Gujarat, India’s westernmost state, indicate that these small tree-dwellers resembled the first primates from as early as 65 million years ago, the scientists report in the October 2016 Journal of Human Evolution.

     These discoveries add to previously reported jaws, teeth and limb bones of four ancient primate species found in the same mine. “The Vastan primates probably approximate a common primate ancestor better than any fossils found previously,” says paleontologist and study co-author Dr. Kenneth Rose of Johns Hopkins University.

     The Vastan animals were about the size of living gray mouse lemurs and dwarf lemurs, weighing roughly 150 to 300 grams (about half a pound), the investigators estimate. 

      Most Vastan creatures possessed a basic climbing ability unlike the more specialized builds of members of the two ancient primate groups that gave rise to present-day primates, the researchers say. One of those groups, omomyids, consisted of relatives of tarsiers, monkeys and apes. 

       The other group, adapoids, included relatives of lemurs, lorises and bushbabies. The Indian primates were tree-dwellers but could not leap from branch to branch like lemurs or ascend trees with the slow-but-sure grips of lorises, the new report concludes.

      Vastan primates probably descended from a common ancestor of omomyids and adapoids, the researchers propose. India was a drifting landmass headed north toward a collision with mainland Asia when the Vastan primates were alive. Isolated on a huge chunk of land, the Indian primates evolved relatively slowly, retaining a great number of ancestral skeletal traits, the researchers propose.

      “It’s possible that India played an important role in primate evolution,” says evolutionary anthropologist Dr. Doug Boyer of Duke University. In 2010, a team led by Boyer reported that a roughly 65-million-year-old fossil found in southern India might be a close relative of the common ancestor of primates, tree shrews and flying lemurs (which glide rather than fly and are not true lemurs).

     One possibility is that primates and their close relatives evolved in isolation on the island continent of India between around 65 million and 55 million years ago, Dr. Boyer suggests. Primates then spread around the world once India joined Asia by about 50(?) million years ago.

     This is a controversial idea. An increasing number of scientists suspect primates originated in Asia. Chinese primate fossils dating to 56 million to 55 million years ago are slightly older than the Vastan primates. The Chinese finds show signs of having been omomyids.

      And in at least one respect, Dr. Boyer says, some of the new Vastan fossils may be more specialized than their discoverers claim. Vastan ankle bones, for instance, look enough like those of modern lemurs to raise doubts that the Indian primates were direct descendants of primate precursors.

      Dr. Dunn, however, regards the overall anatomy of the Vastan fossils as “the most direct evidence we have” that ancestors of early primates lacked lemurs’ leaping abilities, contrary to what some researchers have argued. 

Your thoughts? Omo or Ada? Or?

P.S. My oldest peach tree is loaded with fruit this year! They are just ripening now.

Wednesday, September 7, 2016

Quiescence: Not Just for Popsicles Any More; A Nicaraguan Volcano Goes Quiet Just Before Eruption

      Volcano semiotics indicating when a volcano is going to erupt include seismographs that display an increase in small tremors which might indicate that magma beneath the mountain is moving, a release of volcanic gases like sulfur dioxide and carbon dioxide, and changes in the physical shape of the volcano such as depressions or growths.

      While these clues tell researchers that the forces that fuel eruptions are moving, they don’t necessarily provide a timeline for when the eruptions will occur.

      By looking at the rate at which earthquakes happen in Nicaragua’s Telica Volcano, a team of scientists studying the volcano have discovered a new method of forecasting volcanic explosions. Their study, published this month in Earth and Planetary Science Letters, describes a period of seismic quiescence, or quiet time, that occurs immediately before an individual explosion.

      Volcanic eruptions are generally made up of many different explosions which can span hours, days, or even months. Depending on how much pressure has been building within the volcano, these individual explosions can range from small bursts of steam to giant, gaseous plumes of ash and smoke. Many smaller eruptions, those on the lower end of the Volcanic Explosivity Index (VEI), occur with little consequence to the people living in the region, while the larger explosions can have devastating effects on nearby communities.

      “We first realized the potential impact of our finding as the 2011 eruption of Telica was in progress and we started to understand that there was a pattern of precursory seismic quiescence prior to each explosion”, says Dr. Diana Roman, one of the study’s co-authors. “We were very excited about the forecasting potential of the quiescence at that time, but we had to do quite a lot more work after the eruption was over to understand the phenomenon and its relationship to the volcano's activity.” [One of the only other time I see the word quiescent is on "quiescently frozen popsicles."]

      Of the 50 explosions studied during Telica’s 2011 eruption, 48 of them were preceded by some sort of seismic silence.

      In addition, there appeared to be a correlation between the length of the quiet time and how catastrophic each explosion was. In short—the longer the quiet time, the more volatile each explosion was. Why does this happen?

     The team discovered that the pathways along which the volcanic gases escape become sealed, which builds pressure. The longer these gases spend trapped beneath the surface, the larger and more catastrophic the ensuing eruption is. The researchers suspect that newly formed minerals might block pathways inside the volcano, or possibly the pathways simply collapse, impeding avenues of escape for volcanic gases.

      Although each eruption is different, and so is each volcano, the implications of a study like this could be far-reaching.

      “I think there is great potential for our findings to be used in a real-time monitoring context,” Dr. Roman says, “the quiescence signal is relatively easy to detect as it requires only one seismometer rather than a large network of seismometers, meaning it can be implemented more cheaply.”

The closer scientists get to predicting volcanic eruptions, the more easily people can learn to live along the flanks of volcanoes such as Telica.


Quiescently unfrozen in the Rocky Mountains,

Wednesday, August 31, 2016

One-Syllable State of Maine Rocks: Underappreciated Silurian Age Stones

      Take a close look at these exquisite Silurian rocks from the state of Maine, USA. (How did I just realize Maine is our only monosyllabic state?) The Silurian, an underappreciated time period, without the cachet of say, the younger Jurassic, is part of the Paleozoic era between the Ordovician and Devonian. Silurian rocks are 443 million years to 416 million years old.

A significant evolutionary milestone during the Silurian was the diversification of jawed and bony fishes. 

       Life also began to appear on land during the Silurian in the form of moss-like, vascular land plants that grew beside bodies of water. Small terrestrial arthropods also began to appear.

       These Maine rocks of the Kittery Formation are old. They show the results of millions of years of deposition, igneous activity, faulting, tectonics, and metamorphism. 

      However, in researching this week's topic, I discovered the "Silurians," a fictional race of reptile-like humanoids in the long-running British science fiction tv series Doctor Who? Those first Silurians are depicted as prehistoric and scientifically advanced sentient humanoids who predate the evolution of man.

      The creatures were called Silurians, after their supposed origins in the Silurian period. However, author John Pertwee claims that "properly speaking", the Silurians should have been called the "Eocenes" (part of the much more recent Cenozoic era.)
     Perhaps Dr. Who needed a geologic consultant to the tv show. E. O. Seen and heard? Background music by Diana Ross and the Eocenes?!

Just call me,
Silurian Steph

Bonus question: without googling or duck duck going, name all current countries of only one syllable.

Thursday, August 25, 2016

CRISPR Technology: Palindromic AHA!

      As we discussed last week, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are segments of prokaryotic DNA containing short repetitions of base sequences. 


       CRISPR’s powerful possibilities — even the controversial notions of creating “designer babies” and eradicating entire species — are stunning and sometimes disconcerting.

     So far CRISPR’s biggest impact has been felt in biology labs around the world. The inexpensive, easy-to-use gene editor has made it possible for researchers to delve into fundamental mysteries of life in ways that had been difficult or impossible. Developmental biologist Dr. Robert Reed likens CRISPR to a computer mouse.

       “You can just point it at a place in the genome and you can do anything you want at that spot.”
Anything, that is, as long as it involves cutting DNA. CRISPR/Cas9 in its original incarnation is a homing device (the CRISPR part) that guides molecular scissors (the Cas9 enzyme) to a target section of DNA. Together, they work as a genetic-engineering cruise missile that disables or repairs a gene, or inserts something new where it cuts.

      Even with all the genetic feats the CRISPR/Cas9 system can do, “there were shortcomings. There were things we wanted to do better,” says MIT molecular biologist Dr. Feng Zhang, one of the first scientists to wield the molecular scissors. From his earliest report in 2013 of using CRISPR/Cas9 to cut genes in human and mouse cells, Zhang has described ways to make the system work more precisely and efficiently.

      He isn’t alone. A flurry of papers in the last three years have detailed improvements to the editor. Going even further, a group of scientists, including Zhang, have dreamed up ways to make CRISPR do a toolbox’s worth of jobs.

      Turning CRISPR into a multitasker often starts with dulling the cutting-edge technology’s cutting edge. In many of its new adaptations, the “dead” Cas9

scissors can’t snip DNA. Broken scissors may sound useless, but scientists have upcycled them into chromosome painters, typo-correctors, gene activity stimulators and inhibitors and general genome tinkerers.

      “The original Cas9 is like a Swiss army knife with only one application: It’s a knife,”

      says Dr. Gene Yeo, an RNA biologist at the University of California, San Diego. But Yeo and other researchers have bolted other proteins and chemicals to the dulled blades and transformed the knife into a multifunctional tool.

      Zhang and colleagues are also exploring trading the Cas9 part of the system for other enzymes that might expand the types of manipulations scientists can perform on DNA and other molecules. With the expanded toolbox, researchers may have the power to pry open secrets of cancer and other diseases and answer new questions about biology.
     The genome is like a piano, says Dr. Jonathan Weissman, a biochemist at the University of California, San Francisco. “You can play a huge variety of different music with only 88 keys by how hard you hit the keys, what keys you mix up and the timing.” By dialing down or turning up the activity of combinations of genes at precise times during development, cells are coaxed into becoming hundreds of different types of body cells.

     For the last 20 years, researchers have been learning more about that process by watching when certain genes turn on and off in different cells. Gene activity is controlled by a large variety of proteins known as transcription factors. When and where a transcription factor acts is at least partly determined by chemical tags on DNA and the histone proteins that package it. Those tags are known collectively as epigenetic marks. They work something like the musical score for an orchestra, telling the transcription factor “musicians” which notes to hit and how loudly or softly to play. So far, scientists have only been able to listen to the music.

      With this new research, researchers can create molecules that will change epigenetic notes at any place in the score, Weissman says, allowing researchers to arrange their own music.
Epigenetic marks are alleged to be involved in addiction, cancer, mental illness, obesity, diabetes and heart disease. Scientists haven’t been able to prove that epigenetic marks are really behind these and other ailments, because they could never go into a cell and change just one mark on one gene to see if it really produced a sour note.

      The explosion of new ways to use CRISPR hasn’t ended. “The field is advancing so rapidly,” says Zhang. “Just looking at how far we have come in the last three and a half years, I think what we’ll see coming in the next few years will just be amazing,” according to an article published this week.

What a difference the past 4 years have made in epigenetics!


Wednesday, August 17, 2016

From Fish Fin Rays to Fingers: The Digit-al Age

      One of the major transformations required for the descendants of fish to become creatures that could walk on land was the replacement of long, elegant fin rays by fingers and toes. In the August 17, 2016, issue of Nature, scientists from the U. of Chicago show that the same cells that make fin rays in fish play a central role in forming the fingers and toes of four-legged creatures.

      After 3 years of experiments using new gene-editing techniques and sensitive mapping to label and track developing cells in fish, the researchers describe how the small flexible bones found at the ends of fins are related to fingers and toes, which are more suitable for life on land.

     "When I first saw these results you could have knocked me over with a feather," said the study's senior author, Dr. Neil Shubin, an authority on the transition from fins to limbs.

      "For years," he said, "scientists have thought that fin rays were completely unrelated to fingers and toes, completely dissimilar because one kind of bone is initially formed out of cartilage and the other is formed in simple connective tissue. Our results change that whole idea. We now have a lot of things to rethink."

     To unravel how fins might have transformed into wrists and fingers, the researchers worked mostly with standard zebrafish.

     Dr.Tetsuya Nakamura, used a gene-editing technique, CRISPR/Cas, in zebrafish to delete important genes linked to limb-building, and then selectively bred zebrafish with multiple targeted deletions. He cross bred the fish mutants, a project that began at Woods Hole, Massachusetts.

     The researchers simultaneously refined cell-labeling techniques to map out when and where specific embryonic cells migrated as the animals developed.

     "It was one of those eureka moments," Dr. Andrew Gehrke said. "We found that the cells that mark the wrists and fingers of mice and people were exclusively in the fin rays of fish."

     The team focused on Hox genes, which control the body plan of a growing embryo along the head-to-tail, or shoulder-to-fingertip, axis. Many of these genes are crucial for limb development.
They studied the development of cells, beginning soon after fertilization and followed them as they became part of an adult fin. Previous work has shown that when Hox genes, specifically those related to the wrists and digits of mice (HoxD and HoxA), were deleted, the mice did not develop those structures. When Nakamura deleted those same genes in zebrafish, the long fins rays were greatly reduced.

     "What matters is not what happens when you knock out a single gene but when you do it in combination," Dr. Nakamura explained. "That's where the magic happens."

     The researchers also used a high-energy CT scanner to see the minute structures within the adult zebrafish fin. These can be invisible, even to most traditional microscopes. The scans revealed that fish lacking certain genes lost fin rays, but the small bones made of cartilage fin increased in number.

     The authors hypothesize that the mutants that Nakamura made caused cells to stop migrating from the base of the fin to their usual position near the tip. This inability to migrate meant that there were fewer cells to make fin rays, leaving more cells at the fin base to produce cartilage elements.

     "It really took the combination of labeling and knockouts to convince us that this cellular relationship between fins and limbs was real," Dr. Gehrke said.

     Future research includes new expeditions to find more fossil intermediates -- such as Tiktaalik, a link between primitive fish and the first four-legged animals, discovered by Shubin and others in 2006 -- in the transition from fins to limbs. 

     The researchers are also planning experiments with Hox genes to learn how a common population of cells can form such different structures in fish and humans.

Anything fishy about this story? It's certainly not fin-ished yet. . .

Happy 23rd birthday today, Zoë (8/20/16)! Photo of Zoë in northern Ethiopia, safe and sound.