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.

YouTube+ for Science from PLoS

SciVee is a new site by the great people at PLoS, with support from NSF and San Diego Supercomputer Center. It is very early in the launch of this effort but it looks very promising.

SciVee allows scientists to communicate their work as a multimedia presentation incorporated with the content of their published article. Other scientists can freely view uploaded presentations and engage in virtual discussions with the author and other viewers. SciVee also facilitates the creation of communities around specific articles and keywords. Use this medium to meet peers and future collaborators that share your particular research interests.

Of course plenty of great videos are already online but this looks like another great effort at helping improve communication of scientific ideas by the Public Library of Science. And there are advantages to a community lead by scientists that not only posts videos but encourages scientific discussion on the related matters. I am hopeful (and confident) this will become a great resource.

Related: Science and Engineering Webcast Directory – Stanford Linear Accelerator Center Public Lectures – Google Engineering and Technology Webcasts
Originally I posted this to my employers blog: Engineering and…. It turns out it was made public prematurely – SciVee update.

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.”

Continue reading →

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.
…
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.

Ocean Foam

Cappuccino Coast: The day the Pacific was whipped up into an ocean of froth

One minute a group of teenage surfers were waiting to catch a wave, the next they were swallowed up in a giant bubble bath. The foam was so light that they could puff it out of their hands and watch it float away. It stretched for 30 miles out into the Pacific in a phenomenon not seen at the beach for more than three decades.

Scientists explain that the foam is created by impurities in the ocean, such as salts, chemicals, dead plants, decomposed fish and excretions from seaweed. All are churned up together by powerful currents which cause the water to form bubbles. These bubbles stick to each other as they are carried below the surface by the current towards the shore.

As a wave starts to form on the surface, the motion of the water causes the bubbles to swirl upwards and, massed together, they become foam.
…
As for 12-year-old beachgoer Tom Woods, who has been surfing since he was two, riding a wave was out of the question. “Me and my mates just spent the afternoon leaping about in that stuff,” he said. “It was quite cool to touch and it was really weird. It was like clouds of air – you could hardly feel it.”

Financial Engineering

In addition to this blog I also run the Curious Cat Investing and Economics blog. Still I don’t really understand what financial engineering is. Here is an article from the author of an excellent economics blog – Reverse engineering financial engineering:

Call it the downside of complex financial engineering. That engineering took some risks off the banks balance sheet (literally in some cases), but it also means that no one quite knows where the subprime losses are. And there is a suspicion that some of those losses are hiding in funds that haven’t offered adequate compensation for the risk.

A few months ago a lot of subprime debt could be packaged into a security that was worth more than the sum of its parts (with a bit of help from the credit rating agencies. And this process was widely lauded. The IMF argued that the United States unique skill at creating innovative fixed income “product” was pulling in the capital needed to finance the US current account deficit. The Fed argued that financial innovation allowed the banks to sell risks that they previously might have held on their balance sheet — though it is also worth noting that the banks themselves were big buyers of MBS as well. Risks were divided and then sold to those best able to manage them.

I understand there has been a large move toward using highly complex math for financial strategies. I understand many derivatives and other investment vehicles have been created. I just don’t really get what makes some of it engineering. Creating new financial instruments, I can come close to understand the argument for calling that engineering but still… And I don’t understand why complex accounting often seems to be called engineering instead of accounting. And the portion that is mainly about changing legal classification then isn’t it more legal than engineering (it seems much financial engineering are gimmicks or tricks or… to gain favorable legal classification for tax… purposes).

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.”

Vertical Rotation Personal Windmill

New wind turbine spins success for winning student

Ben Storan, a student graduating with an MA in Industrial Design Engineering from the Royal College of Art (RCA), has been working for the past year in conjunction with Imperial College to design an affordable personal wind turbine suited to the urban environment.

The result is a unique design which uses vertical, rather than traditional horizontal, rotation. This feature gives a slower rotational speed, which allows the turbine to capture more energy from turbulent air flow, common to urban environments. It also means quieter operation. As a result, it is able to generate more energy than domestic models currently on the market. Similarly sized existing personal wind turbines claim to generate 1kW at a wind speed of 12 m/s, but typically produce just 40% of what is claimed. Ben’s design should realistically produce 3 times that (1.2kW) of those currently on the market.

Sexy Math

Mean Girls:

British researchers, stated that men had 12.7 heterosexual partners in their lifetimes and women had 6.5.” These numbers, though Kolata doesn’t say so, are means, not medians. In this case, it’s indeed mathematically impossible that the numbers are correct. The medians in the British sample? Seven and four, same as in the American study—so you can stop worrying about a transatlantic promiscuity gap.

“It is logically impossible for heterosexual men to have more partners on average than heterosexual women,” she explains. “Those survey results cannot be correct.” Kolata even quotes a theorem to this effect, backed up by mathematician David Gale of Berkeley: The average number of partners has to be the same for men and women.

This article makes several good mathematical and scientific points, including the dangers of trusting reports by participants. Also I can see if this page is more popular than some of the other math posts. For awhile now I have noticed “sex 100” showing up as one of the terms guiding the most visitors to this site. I wondered what that could be – I just took a look: Bdelloid Rotifers Abandoned Sex 100 Million Years Ago. I think maybe those searchers didn’t exactly find what they wanted.