Category Archives: Science

One Species’ Genome Discovered Inside Another’s

Video describing genome inside genome Watch video of Professor Werren describing the genome-in-a-genome at the University of Rochester.

More incredible gene research. Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. The research, reported in today’s Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits.

“This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.”

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Displaying Data Well

Data is often displayed poorly leaving it difficult to see what is important. By displaying data well the important facts should leap off the page and into the viewers mind. Edward Tufte is an expert on the topic and has published great books. I strongly recommend reading at least one (and if you do I think the odds are good you will read more): Beautiful Evidence, The Visual Display of Quantitative Information, Envisioning Information and Visual Explanations.

Smashing magazine has some nice examples of good display techniques in Data Visualization: Modern Approaches. I don’t like all the examples they show but it does provide some help by showing some creative ways to display data.

Mars Rovers Getting Ready for Another Adventure

Mars Rover

Mars rovers begin to stir as dust storms recede

NASA’s twin Mars rovers Spirit and Opportunity are starting to move again after being immobilised for six weeks by severe dust storms. The storms hit in late June, just as Opportunity was poised to enter the 800-metre-wide Victoria crater, which may contain crucial geological records of past conditions on Mars.

Lofting dust high in the atmosphere, the storms blocked precious sunlight needed for the rover solar panels to generate power. Both rovers had to stop driving, and Opportunity was so starved of power that its handlers worried it might freeze to death during the cold Martian night. Now, the storms have finally receded and both rovers are about to start driving towards much-anticipated targets.
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Opportunity is getting about 300 watt-hours of energy per day, more than twice the level it was getting during the worst part of the storms. But it is still not enough to start the descent into the crater, Arvidson says: “We want to make sure if we have some mobility problems that there’s energy to spare to get out of the problem areas.”

These rovers just keep going. From a NASA press release last October: “NASA’s long-lived Mars Exploration Rover Spirit will finish its 1,000th Martian day Thursday, continuing a successful mission originally planned for 90 Martian days.”

Image credit: NASA/JPL Artist’s concept of the Mars Exploration Rover on Mars.High Resolution Image

Science Journal Publishers Stay Stupid

Science publishers get even stupider by Andrew Leonard:

The American Association of Publishers and everyone associated with it should be ashamed of trying to protect their profit margins by slandering the open access movement as government intervention and censorship. Research paid for with government funds should be freely accessible to the general public.

I wish it was amazing that these people have so little grasp of what has been going on in the world the last 5 years (but I must say such failure to adapt seems to be a common trait in too many organizations). Previously I have posted on the importance of continuing the scientific tradition of open debate and open access. In the past there have been distribution complexities that made paid journals an acceptable compromise. That people working at journals don’t see that the internet changes that is going to lead to their rapid irrelevance. They had to figure this out a couple of years ago. Given they still haven’t, I must say that they really don’t seem to have much understanding of science or modern communication methods. Given their industry that is sad. It is time for the scientific community to give up on these journals and start looking to move to work with new organizations that will encourage scientific communication and advancement (PLoS – arXiv.org – Open Access Engineering Journals) and leave those that seek to keep outdated practices to go out of business.

“It is not necessary to change. Survival is not mandatory.” Dr. W. Edwards Deming

I do object to scientific knowledge being kept out of the scientific and public community. The ability to use the internet to more effectively communicate new knowledge should not be sacrificed to protect the old model journals had for sustaining themselves. They should find a way to fund themselves and make their material available for free on the internet (I think some delay for free public access would be fine – the shorter the delay the better). Or they should be replaced by others that do so.

Studying Martian Soil for Evidence of Microbial Life

Study: Martian soil may contain life

The search for life on Mars appeared to hit a dead end in 1976 when Viking landers touched down on the red planet and failed to detect biological activity. But Joop Houtkooper of the University of Giessen, Germany, said on Friday the spacecraft may in fact have found signs of a weird life form based on hydrogen peroxide on the subfreezing, arid Martian surface.

His analysis of one of the experiments carried out by the Viking spacecraft suggests that 0.1 percent of the Martian soil could be of biological origin. That is roughly comparable to biomass levels found in some Antarctic permafrost, home to a range of hardy bacteria and lichen. “It is interesting because one part per thousand is not a small amount,” Houtkooper said in a telephone interview.

“We will have to find confirmatory evidence and see what kind of microbes these are and whether they are related to terrestrial microbes. It is a possibility that life has been transported from Earth to Mars or vice versa a long time ago.”

Interesting, certainly far from convincing evidence but still fun speculation. Claim of Martian Life Called ‘Bogus’:

Norman Pace, a microbiologist at the University of Colorado, is skeptical of the new claims. “It sounds bogus to me,” Pace told SPACE.com. “I don’t consider the chemical results to be particularly credible in light of the harsh conditions that Mars offers.”

Mining the Moon

Mining the Moon by Mark Williams:

At the 21st century’s start, few would have predicted that by 2007, a second race for the moon would be under way. Yet the signs are that this is now the case. Furthermore, in today’s moon race, unlike the one that took place between the United States and the U.S.S.R. in the 1960s, a full roster of 21st-century global powers, including China and India, are competing.

Even more surprising is that one reason for much of the interest appears to be plans to mine helium-3–purportedly an ideal fuel for fusion reactors but almost unavailable on Earth–from the moon’s surface
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But a serious critic has charged that in reality, He3-based fusion isn’t even a feasible option. In the August issue of Physics World, theoretical physicist Frank Close, at Oxford in the UK, has published an article called “Fears Over Factoids” in which, among other things, he summarizes some claims of the “helium aficionados,” then dismisses those claims as essentially fantasy.

As I stated in January in Helium-3 Fusion Reactor: “This sounds pretty incredible to me and I find the claims of using fuel from the Moon economically to power our needs on Earth. Still it is interesting and just because it sounds fantastic does not mean it can’t be true. But I am skeptical.”

Textbook Revolution

Textbook Revolution is a resource on free textbooks and free related course materials. In general, I must say the prices of textbooks seem crazy. This is another tool great open access resource.

At Textbook Revolution, you’ll find links to textbooks and select educational resources of all kinds. Some of the books are PDF files, others are viewable only online as e-books. Most books are aimed at undergraduates, but there are at least a few resources at every level, from kindergarten to post-doc. All of the books are offered for free by their respective copyright holders for online viewing. Beyond that, each book is as individual as the author behind it.

Some examples: The Scientist and Engineer’s Guide to Digital Signal Processing by Steven W. Smith; Light and Matter by Benjamin Crowell; A First Course in Linear Algebra by Robert A Beeze; Programming Ruby: The Pragmatic Programmer’s Guide by
Dave Thomas and Introduction to Statistical Thought by Michael Lavine.

While on the subject of textbooks, I will plug my father’s book: Statistics for Experimenters – it is my blog so I get to do what I want 🙂

Peak Soil

An interesting article. Obvious the author has a biased viewpoint (that doesn’t mean the conclusions are wrong but it certainly can make one cautious – just as if a drug company shows results that their drug is effective or safe – you just have to pay a bit more attention…). I would be interested in others thoughts on this. My perception (though it is just an opinion based on limited facts) is that topsoil loss is a problem and that using corn for ethanol is more a federal government payoff to buy votes than a wise national policy. I am less inclined to accept some of the more extreme suggestions in the article. Peak Soil: Why cellulosic ethanol, biofuels are unsustainable and a threat to America

“The nation that destroys its soil destroys itself.” – President Franklin D. Roosevelt
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When you take out more nutrients and organic matter from the soil than you put back in, you are “mining” the topsoil. The organic matter is especially important, since that’s what prevents erosion, improves soil structure, health, water retention, and gives the next crop its nutrition. Modern agriculture only addresses the nutritional component by adding fossil-fuel based fertilizers, and because the soil is unhealthy from a lack of organic matter, copes with insects and disease with oil-based pesticides.

I believe it makes sense to research things like bio-fuels. However I am not convinced massive payments to the political well connected is a wise course of action.

More on Amazing Aerogel

We added a post on aerogel earlier this month. Here is another article on the incredible substance – Scientists hail ‘frozen smoke’ as material that will change world:

It is expected to rank alongside wonder products from previous generations such as Bakelite in the 1930s, carbon fibre in the 1980s and silicone in the 1990s. Mercouri Kanatzidis, a chemistry professor at Northwestern University in Evanston, Illinois, said: “It is an amazing material. It has the lowest density of any product known to man, yet at the same time it can do so much. I can see aerogel being used for everything from filtering polluted water to insulating against extreme temperatures and even for jewellery.”
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It also has green credentials. Aerogel is described by scientists as the “ultimate sponge”, with millions of tiny pores on its surface making it ideal for absorbing pollutants in water. Kanatzidis has created a new version of aerogel designed to mop up lead and mercury from water. Other versions are designed to absorb oil spills.

Megaflood Created the English Channel

Ancient Megaflood Made Britain an Island, Study Says

“It is probably one of the largest floods ever identified,” said Phillip Gibbard, a geographer at the University of Cambridge who wasn’t involved in the study. At its peak, the flood would have discharged water at a rate of about 264 million gallons (a million cubic meters) a second, gushing at speeds of up to 62 miles (100 kilometers) an hour, the researchers say. This is roughly equivalent to ten times the combined flow rate of all the rivers in the world.

In addition to making Britain an island, the authors add, the huge flood had wide-ranging environmental consequences. For example, the gigantic pulse of freshwater entering the Atlantic Ocean likely caused a period of climate cooling in the Northern Hemisphere, Gibbard said. “The introduction of ice and freshwater into an ocean drives climate oscillations and causes marked cooling events,” he explained.

The flood also marooned many animals and plants, so those species gradually evolved into different forms than their mainland cousins.

via: Pre-Chunnel Flood