Category Archives: Science

Communicating Science to the Public

Webcast above: Speaking Science 2.0 by Matthew Nisbet, School of Communication, American University, and Chris Mooney, Washington Correspondent, Seed Magazine, speak at the AIBS annual meeting, May 2007, in Washington DC. They discuss how to improve the transfer of science knowledge to the public (an important topic and one I am interested in). More on The American Institute of Biological Sciences conference: Evolutionary Biology and Human Health.

via: Framing Science

Open Access and PLoS

In An Open Mouse, Carl Zimmer discusses the conflict between closed journals and those that support open access.

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it.

His post mentions the recent bad publicity Wiley received. It seems to me the Journals still don’t understand that their copyright of research results paid for by public funds are not going to continue. And that open access science is clearly the way of the future that their continued failure to deal with is increasing the odds monthly that they will find themselves on the outside of those practicing science in the 21st Century.

PLoS on the other hand recently hired Bora Zivkovic as PLoS ONE Online Community Manager. He will be great and continue to build PLoS into an organization supporting free and open science. I loved PLoS proactive action recounted by Bora, he posted that he was interested in the job:

Next morning, I woke up to a comment by the Managing Editor of PLoS ONE asking if my blog-post should be considered as a formal job application. My comment in response was a Yes.

Evolution In Action

the way they watched the process was to sequence the whole genome of each bacterial isolate. What they found were a total of 35 mutations, which developed sequentially as the treatment continued (and the levels of resistance rose). Here’s natural selection, operating in real time, under the strongest magnifying glass available. And it’s in the service of a potentially serious problem, since resistant bacteria are no joke. (Reading between the lines of the PNAS abstract, for example, it appears that the patient involved in this study may well not have survived).

The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.

Very interesting. He is exactly right that the technology advances continuing at an amazing pace allow for experiments we (at least I) can’t even imagine today to become common in just a few years. And the insights from those experiments will allow us to think of new experiments… Wonderful.

Finding Open Scientific Papers

Sandra Porter has posted a series of posts on finding scientific papers for free: A day in the life of an English physician – What’s the best way to find free scientific publications? – My new favorite method – one more experiment

via: Finding scientific papers for free

Female Sharks Can Reproduce Alone

Female Sharks Can Reproduce Alone, Researchers Find

A team of American and Irish researchers have discovered that some female sharks can reproduce without having sex, the first time that scientists have found the unusual capacity in such an ancient vertebrate species. The[y] report that sharks can reproduce asexually through the process known as parthenogenesis
…
Though the three females had been caught before they reached sexual maturity and held in captivity for more than three years, researchers initially thought one had stored sperm from a male shark before fertilizing an egg. But the team — which included scientists at Nova Southeastern University in Florida, Queen’s University Belfast and the zoo — determined that the baby shark’s genetic makeup perfectly matched one of the females in the tank, with no sign of a male parent.

Mahmood Shivji — Nova Southeastern’s Guy Harvey Research Institute director and one of the paper’s authors — said that he and his colleagues determined that a byproduct formed when sharks produce eggs, known as a sister polar body, had fused with an unfertilized egg to produce the baby shark, whose DNA had only half as much genetic variability as the mother.

Chemistry of Common Items

The American Chemistry Society offers interesting articles on the chemistry of everyday products including: amber, henna, catnip and honey:

To make this delicious treat, foraging bees start out by guzzling nectar, a dilute solution of sugars in flowers. Then, they mix the nectar with enzymes in their stomachlike honey sacs. Back at the hive, the foragers pass the digested material to house bees who reduce the moisture content of the mixture by ingesting and regurgitating it. They then deposit concentrated drops into honeycomb cells. Over the next few days, bees fan the fluid with their wings to further concentrate it, and finally, they cap the cells with wax. At the same time, enzyme-mediated changes produce a range of sugars and acids in the honey.

Bee enzymes also show up in the finished product. Invertase is the most critical. It splits the sucrose in the nectar into fructose and glucose and also produces some erlose. Another enzyme, glucose oxidase, converts glucose to gluconolactone, which is then hydrolyzed to give gluconic acid, the principal acid in honey. Formic, acetic, butyric, and lactic acids are also found in honey, which explains why its pH typically measures 3.8-4.0 and bacteria have a hard time growing in it.

Engineering, Math and Physics Applets

Java applets illustrating concepts in math, physics and engineering including: Coupled Oscillations, Digital Filters, 3-D Magnetostatic Fields and Ordinary Differential Equations.

CERN Prepares for LHC Operations

A Giant Takes On Physics’ Biggest Questions

The physicists, wearing hardhats, kneepads and safety harnesses, are scrambling like Spiderman over this assembly, appropriately named Atlas, ducking under waterfalls of cables and tubes and crawling into hidden room-size cavities stuffed with electronics.

They are getting ready to see the universe born again. Again and again and again – 30 million times a second, in fact.

Starting sometime next summer if all goes to plan, subatomic particles will begin shooting around a 17-mile underground ring stretching from the European Center for Nuclear Research, or CERN, near Geneva, into France and back again – luckily without having to submit to customs inspections.

Crashing together in the bowels of Atlas and similar contraptions spaced around the ring, the particles will produce tiny fireballs of primordial energy, recreating conditions that last prevailed when the universe was less than a trillionth of a second old.

Wow that sounds impressive. Oh yeah, it is impressive. Good writing too.

Hot Ice Planet

Scooped!:

The planet has a mass of 23 Earth-masses and an orbital period of 2.64385 days. It orbits a red dwarf star 33 light years away. The temperature on the planet is somewhere in the oven-cleaning neighborhood of 600K (327K, 620F). No habitability news stories on CNN for this fine fellow. The transit depth is a healthy 0.6%, which implies that the the planet’s radius is ~25,000 km. That’s four times that of the Earth, and essentially identical to the 24,764 km radius of Neptune.

Astronomers Detect Shadow Of Water World In Front Of Nearby Star:

As the planet is close to its host star, its surface temperature is expected to be at least 300 C (600 F). The water in its atmosphere would therefore be in the form of steam. Inside, the water is crushed under intense pressure and adopts states unknown on Earth, except in physicist’s laboratories. Says FrÃ©dÃ©ric Pont: “water has more than a dozen solid states, only one of which is our familiar ice. Under very high pressure, water turns into other solid states denser than both ice and liquid water, just as carbon transforms into diamond under extreme pressures. Physicists call these exotic forms of water ‘Ice VII’ and ‘Ice X’. If Earth’s oceans were much deeper, there would be such exotic forms of solid water at the bottom.” Inside GJ 436’s planet, this strange ice is moreover heated to many hundred degrees.

Bacterium Living with High Level Radiation

Organism found at SRS amazes scientific world by Rob Pavey

In addition to thriving in the face of normally-lethal radiation, the organism also demonstrates remarkable survival characteristics in terms of its DNA. Humans and most organisms can tolerate few breaks in DNA molecules, he said, but kineococcus radiotolerans has the ability to reassemble itself.

“With this organism, we can take an intact DNA molecule, blast it into little pieces, and in five to six hours the organism is restored and growing normally again,” Dr. Bagwell said. Dr. Bagwell and others who have studied the organism hope further research will yield clues that could aid in medical research, cancer studies and other areas.

“There’s a lot of excitement about this organism because of its ability to withstand tremendous abuse,” he said. “What we don’t know is how it does these things – and what more it can do. That’s the direction we’re going now.”

Related: What is an Extremophile? – more info on Kineococcus radiotolerans