Category Archives: Students

Items for students and others, interested in learning about science and engineering and the application of science in our lives. We post many of the general interest items here.

Friday Fun: Penguin Evades Orcas

A penguin takes sanctuary on a boat while killer whales circle.

Ender in Exile by Orson Scott Card

Ender in Exile by Orson Scott Card has just been published. It is the ninth book in the Ender Wiggen series that began with Ender’s Game (Hugo and Nebula book award winner). I love the Ender series and have a table showing the sequence of the books. The books have not been published in the order of events in the fictional world. Ender in Exile is directly follows Ender’s Game (which makes it 3rd in story order – since Ender’s Shadow took place concurrently with Ender’s Game).

You can listen to Orson Scott Card read from Ender in Exile.

I include this post because I enjoyed the book. It doesn’t really have much to do with science or engineering but here is a quote from the book (page 106): “Besides, that’s what science was – the sharing of information the pooling of knowledge. That’s my gene pool, Afriama, he thought. The meme pool, the collective knowledge of science. What I discover here, what I learn, the problems I solve – those will be my children.”

Enjoy the book, and if you have not read Ender’s Game I highly recommend it. You can read the original Ender’s Game short story online. And if you haven’t read The Investment Counselor (about Jane, Ender’s computer companion) it is excellent (included in First Meetings in Ender’s Universe)

DoE: Minority Science and Engineering Improvement Program

The United States Department of Education’s Minority Science and Engineering Improvement Program (MSEIP) provides funds to schools to provide awards to students. 20 new awards (average value of $139,000) were awarded this year. That brings total funding this year to 71 awards (50 continue from previous years). Institutions recieving funds include: Clark Atlanta University, Rust College, New Mexico State University, Spelman College, Virginia State University and the College of Menominee Nation.

The program is designed to effect long-range improvement in science at predominantly minority and engineering education programs to increase the participation of underrepresented ethnic minorities, particularly minority women, into scientific and technological careers.

Wiley College, one of the new recipients, aims to increase the number of science majors, especially in the fields of biology and chemistry. A key feature of this grant is the creation of a high school science competition that will allow local and regional high school students to visit the campus and compete in a variety of scientific events.

This event will bring five area high schools together to compete in ten scientific events based on biology, chemistry, mathematics and physics. Individual first-place winners will be given scholarships to Wiley College. There will also be an overall grand champion awarded. This event will allow high school students to experience life at Wiley College and the possibilities of a career in science.

“This event not only gives students a financial reason to enroll at Wiley, but also allows them to become familiar with the campus and its faculty and students, said Dr. Shumate. “This grant also furthers a connection between Wiley and both the University of Texas at Dallas and the University of Arkansas, allowing current Wiley students to attend these schools in the summer for biomedical research.”

Wiley hosts HS science competition Saturday

Looking for Signs of Dark Matter Over Antarctica

Dark Matter Proof Found Over Antarctica?

High-energy electrons captured over Antarctica could reveal the presence of a nearby but mysterious astrophysical object that’s bombarding Earth with cosmic rays, researchers say. Or the electrons may be the long-awaited physical evidence of elusive dark matter.

Either way, the unusual particles are exciting for astrophysicists, who say they could someday confirm or deny decades of unproven theories. “In the first case, we have now seen for the first time a nearby source of cosmic rays.
…
Cosmic rays are not beams per se but are any protons, electrons, and other subatomic particles that careen toward Earth from a variety of sources, including the supernova explosions that mark the deaths of stars.

Most of the cosmic electrons that reach Earth are low-energy, because the highest-energy ones fizzle the fastest and don’t last long enough to get here.

Scientists With Lots of Monitors Onboard Ship

photo of computer monitors onboard ship

Fun blog by Linds, a geophysicist, with fun name and tagline: PhD = Pretty huge Dork There’s no crying in grad school! I enjoy including some posts on scientists at work (and plan on trying to intentionally do more of that). The photo shows her office onboard ship – pretty impressive. I thought this monitor was cool.

The boat is a steel monster about 400 feet long. There’s three decks, with cabins, the galley and mess hall, a few different labs, a movie room, reading room and a weight room with white padded walls. It’s all very “Life Aquatic“, if you get the reference. [those that don’t follow the link its a crazy movie – John]
…
We have been in transit for the past three days, getting our computers and systems up and running. We arrive at our first deployment spot tomorrow morning at 5:30 am. That is when we’ll put our first ocean bottom seismometer (OBS) down. The OBS itself is a sphere about 16 inches in diameter made of inch thick glass–these suckers are heavy! It’s vacuum sealed with the instrumentation inside and attached to an anchor. When we are done with the survey, the sphere is timed to detach from the anchor and it’ll float to the surface of the water. Our boat will pull up alongside it and we’ll scoop it out with a net and crane.
…
woke up today at 3am to get ready for my first watch. We definitely have the worst seas that we have had so far. We are definitely pitching and rolling out here! We deployed our first OBS at 5am and are doing about 1 instrument/hr for the next 24 hours.

Those snippets are from various posts on the blog. Another from earlier:

But there is recent good news: that lone female professor (who is an amazing researcher and is highly respected in the field, chairs many committees both nationally and within the department and was president of the Geological Society of America in the 90’s) has been named the new department chair. I think this move is important in encouraging talented women scientists to apply for positions within the department and shows dedication on the part of the higher-ups to highlighting ‘diversity’ as a priority.

Easier Way to Make Coal Cleaner

MIT has an Energy “Manhattan project”. The USA has a huge amount of coal, if we ever can figure out how to make it clean that will be a huge benefit (though I have my doubts we can really make it clean enough). easier way to make coal cleaner

“Our approach — ‘partial capture’ — can get CO2 emissions from coal-burning plants down to emissions levels of natural gas power plants,” said Ashleigh Hildebrand, a graduate student in chemical engineering and the Technology and Policy Program. “Policies such as California’s Emissions Performance Standards could be met by coal plants using partial capture rather than having to rely solely on natural gas, which is increasingly imported and subject to high and volatile prices.”
…
The researchers conclude that as a near-term measure, partial capture looks promising. New coal plants with lower CO2 emissions would generate much-needed electricity while also demonstrating carbon capture and providing a setting for testing CO2 storage — steps that will accelerate the large-scale deployment of full capture in the future.

How Bleach Kills Bacteria

Developed more than 200 years ago and found in households around the world, chlorine bleach is among the most widely used disinfectants, yet scientists never have understood exactly how the familiar product kills bacteria. In fact, Hypochlorite, the active ingredient of household bleach, attacks essential bacterial proteins, ultimately killing the bugs.

“As so often happens in science, we did not set out to address this question,” said Jakob, an associate professor of molecular, cellular and developmental biology. “But when we stumbled on the answer midway through a different project, we were all very excited.”

Jakob and her team were studying a bacterial protein known as heat shock protein 33 (Hsp33), which is classified as a molecular chaperone. The main job of chaperones is to protect proteins from unfavorable interactions, a function that’s particularly important when cells are under conditions of stress, such as the high temperatures that result from fever.

“At high temperatures, proteins begin to lose their three-dimensional molecular structure and start to clump together and form large, insoluble aggregates, just like when you boil an egg,” said lead author Jeannette Winter, who was a postdoctoral fellow in Jakob’s lab. And like eggs, which once boiled never turn liquid again, aggregated proteins usually remain insoluble, and the stressed cells eventually die.

Jakob and her research team figured out that bleach and high temperatures have very similar effects on proteins. Just like heat, the hypochlorite in bleach causes proteins to lose their structure and form large aggregates.

These findings are not only important for understanding how bleach keeps our kitchen countertops sanitary, but they may lead to insights into how we fight off bacterial infections. Our own immune cells produce significant amounts of hypochlorite as a first line of defense to kill invading microorganisms. Unfortunately, hypochlorite damages not just bacterial cells, but ours as well. It is the uncontrolled production of hypochlorite acid that is thought to cause tissue damage at sites of chronic inflammation.

How did studying the protein Hsp33 lead to the bleach discovery? The researchers learned that hypochlorite, rather than damaging Hsp33 as it does most proteins, actually revs up the molecular chaperone. When bacteria encounter the disinfectant, Hsp33 jumps into action to protect bacterial proteins against bleach-induced aggregation.

“With Hsp33, bacteria have evolved a very clever system that directly senses the insult, responds to it and increases the bacteria’s resistance to bleach,” Jakob said.

New Supercomputer for Science Research

“Jaguar is one of science’s newest and most formidable tools for advancement in science and engineering,” said Dr. Raymond L. Orbach, DOE.s Under Secretary for Science. The new capability will be added to resources available to science and engineering researchers in the USA.

80 percent of the Leadership Computing Facility resources are allocated through the United States Department of Energy’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, a competitively selected, peer reviewed process open to researchers from universities, industry, government and non-profit organizations. Scientists and engineers at DOE’s Oak Ridge National Laboratory are finding an increasing variety of uses for the Cray XT system. A recent report identified 10 breakthroughs in U.S. computational science during the past year. Six of the breakthroughs involved research conducted with the Jaguar supercomputer, including a first-of-its-kind simulation of combustion processes that will be used to design more efficient automobile engines. Read the computational science report. Read full press release.

ORNL’s Jaguar fastest computer for science research

Jaguar will be used for studies of global climate change, as well as development of alternative energy sources and other types of scientific problem-solving that previously could not be attempted.

Zacharia said ORNL’s Jaguar was upgraded by adding 200 Cray XT5 cabinets – loaded with AMD quadcore processors and Cray SeaStar interconnects – to the computer’s existing 84 Cray XT4 cabinets. The combined machine resulted in the new standard for computational science.

The peak operating speed is apparently just below that of Los Alamos National Laboratory’s IBM Roadrunner system, which is designed for 1.7 petaflops. But the Jaguar reportedly has triple the memory of Roadrunner and much broader research potential.
…
Because the Jaguar has come online sooner than expected, Zacharia said an alert was sent to top U.S. scientists inviting them to apply for early access to the Oak Ridge computer. Their scientific proposals will be reviewed on an accelerated timetable, he said.

The peak capability of 1.64 petaflops is attributed to 1.384 petaflops from the new Cray XT5, combined with 0.266 petaflops from the existing Cray XT4 system, Zacharia said.

How fast is a quadrillion calculations per second? “One way to understand the speed is by analogy,” Zacharia said recently. “It would take the entire population of the Earth (more than 6 billion people), each of us working a handheld calculator at the rate of one second per calculation, more than 460 years to do what Jaguar at a quadrillion can do in one day.”

Genes Counter a Bacterial Attack

Gene against bacterial attack unravelled

Humans have an innate defence system against deadly bacteria. However, how the step from gene to anti-bacterial effect occurs in the body is not yet known. To date, B. Pseudomallei, a bacterium suitable for bioweapons, had managed to elude medics. It can remain hidden in the human body for many years without being detected by the immune system. The bacteria can suddenly become activated and spread throughout the body, resulting in the patient dying from blood poisoning. AMC physician Joost Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless.

Wiersinga focussed on the so-called Toll-like receptors. These are the proteins that initiate the fight against pathogens. There are currently ten known Toll-like receptors which are located on the outside of immune cells, our body’s defence system. The toll-like receptors jointly function as a 10-figure alarm code. Upon coming into contact with the immune cell each bacterium enters its own Toll code. For known pathogens this sets off an alarm in the immune system and the defence mechanism is activated. Yet B. pseudomallei fools the system by entering the code of a harmless bacterium. As a result the body’s defence system remains on standby.

Yet some people are resistant: they become infected but not ill. Wiersinga found a genetic cause for this resistance. He discovered which toll receptor can fend off B. pseudomallei. He did this by rearing mice DNA in which the gene for Toll2 production was switched on and off. ‘The group where the gene for Toll2 was switched off, survived the bacterial infection’, says Wiersinga. ‘The other receptor that we investigated, Toll4, had no effect – even though for the past ten years medics had regarded this as the most important receptor.’ The ultimate aim of this study is to develop a vaccine.

PLoS paper: MyD88 Dependent Signaling Contributes to Protective Host Defense against Burkholderia pseudomallei

Marine Plankton From 100 Million Years Ago Found in Amber

photo of foraminifer in amber

Marine microorganisms have been found in amber dating from the middle of the Cretaceous period. The fossils were collected in Charente, in France. This completely unexpected discovery will deepen our understanding of these lost marine species as well as providing precious data about the coastal environment of Western France during the Cretaceous. This work was carried out by researchers at the GÃ©osciences Rennes laboratory, together with researchers from the PalÃ©obiodiversitÃ© et PalÃ©oenvironnement laboratory in Paris and the Centre de GÃ©ochimie de la Surface in Strasbourg.

Amber is a fossil resin with a reputation for preserving even the most minute details of insects and other terrestrial arthropods (spiders, scorpions, mites) that lived in resiniferous trees. The forest-based provenance of amber in theory makes it impossible for marine animals to be trapped in the resin. Nonetheless, researchers from the GÃ©osciences Rennes laboratory have discovered various inclusions of marine plankton in amber from the Mid-Cretaceous (100 to 98 million years ago). These micro-organisms are found in just a few pieces of amber among the thousands that have been studied, but show a remarkable diversity: unicellular algae, mainly diatoms found in large numbers, traces of animal plankton, such as radiolaria and a foraminifer, spiny skeletons of sponges and of echinoderms.

Foraminifera (the photo shows one in Amber) are amoeboid protists with reticulating pseudopods, fine strands of cytoplasm that branch and merge to form a dynamic net.[1] They typically produce a test, or shell, which can have either one or multiple chambers, some becoming quite elaborate in structure.[2] These shells are made of calcium carbonate (CaCO3) or agglutinated sediment particles. About 275,000 species are recognized, both living and fossil.[citation needed] They are usually less than 1 mm in size.”

Carried out together with researchers at the MusÃ©um national d’histoire naturelle, the study of diatoms pushed back by 10 to 30 million years the known date for the appearance of certain marine forms of this type of algae. This new information, taken together with recent data on molecular phylogeny, marks a huge advance in our understanding of the complex evolutionary history of diatoms.

The presence of these marine organisms in the amber is an ecological paradox. How did these marine species become stuck and then trapped in the conifers’ resin? The most likely scenario is that the forest producing the amber was very close to the coast, potentially shrouded by plankton-bearing mist or flooded by sea water during storms.

The preservation of marine organisms in amber is an exceptional asset, allowing us to deepen our understanding of these lost species and to have a clear idea about the coastal environment of Western France during the Cretaceous.

press release