Tag Archives: research

Scientist Clarifies ‘Sexy’ News Story from the Telegraph

To wrap up SCIE 300, I have found a recent sensationalized news story, which involves blogging and commenting online!

Water Sampling Probe used during the GOS. Photo: J. Craig Venter Institute

To analyze the DNA of microbes in the oceans, scientists at the J. Craig Venter Institute ventured on the Global Ocean Sampling (GOS) Expedition. In fact, one data collection voyage involved navigating the oceans for over two years! The expeditions have produced an immense data set of DNA sequences.

In search of unusual genes, researchers found new DNA sequences in the GOS data set that were not present in known organisms or viruses. Currently, the tree of life has three major branches or divisions: bacteria, eukarya, and archaea. These sequences formed groups that branched outside of known divisions in the tree of life.  Researchers proposed that the new groups, or lineages, emerged from four possibilities. The two most likely explanations are that the lineages are from unknown viruses or a fourth major branch on the tree of life. Dr. Jonathan Eisen, from U.C. Davis and one of the paper’s authors, believes the former is more probable.

Interestingly, Dr. Eisen and his colleagues decided to forgo a formal university press release for their paper. Instead, Dr. Eisen wrote his own ‘press release’ on his blog, The Tree of Life. He feared that the results of the paper would become overstated in the press, through communication, or even in his own blog post.

Newsy.com video coverage of the research:

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The research was able to make waves in the media and the Telegraph in the UK published an article online with the sexy headline, “Scientist finds a whole new ‘domain’ of life”. Richard Alleyne, the author of the news article, may not have written the headline, but the body of the article did contain inaccuracies. For example, Alleyne had written that the technique used to analyze the DNA was named by the researchers themselves, which was not the case. This was actually the first time the technique was used on a large scale basis.

Dr. Eisen was quick to respond to the misleading headline and inaccuracies within the news article. In the article’s comments section, he noted three of the main errors and provided corrections. Dr. Eisen clarified that a new domain of life is only one of the possible explanations for the findings and not a conclusive result. There have not been any corrections made to the news article yet, but I am curious to see how this will play out!

o The Global Ocean Sampling (GOS) Expedition is a venture by scientists at the J. Craig Venter Institute to analyze the DNA of microbes across the oceans. In fact, one data collection voyage involved navigating the oceans for over two years! The expeditions have produced an immense dataset of DNA sequences.

BC killer whales can’t hear each other!

I spent much of 2010/2011 working on a research project so thought that I would use this ultimate SCIE300 blog post to tell you all about it.

Last September, myself and four others in UBC Environmental Science were put on team and instructed to research whatever environmental science topic we wanted. We were all broadly interested in researching some sort of ecological impact of the Gateway Program, BC’s massive plan for highway and port expansions. We spent first semester narrowing in on a more specific area. Eventually, we landed our focus on the impacts of increasing commercial shipping traffic on the Southern Resident killer whales (SRKW). This population is designated as endangered by the Species at Risk Act and has been in decline over the past several decades.

Photo: Minette Layne on Flickr

This semester, we went into a research paper-reading frenzy on everything and anything to do with killer whales, ships, and killer whales and ships in order to find a manageable gap in the understanding of commercial ship impacts on the SRKW we could work to fill. We soon found that the influence of commercial shipping sound in the SRKW critical habitat — area identified as especially important for the well-being of this species — is little understood.

Also at around this time, a lawsuit led by several environmental groups against the Department of Fisheries and Oceans (DFO) was in the midst of unfolding. Team Enviro had taken DFO to court for failing to protect the SRKW critical habitat (which DFO is legally obliged to protect), and in December 2010, the court ruled against DFO. Noise pollution — along with food availability and toxic pollution — were among the key areas DFO was found to be failing to address. So, knowing that DFO might be considering doing a better job of safe-gaurding the critical habitat, we wanted to conduct research that could inform recommendations to lessen noise impacts on the SRKW.

We got to work using GIS analysis to map out areas of sound influence in the SRKW habitat, identifying spots where the killer whales’ ability to communicate was compromised. In addition, we mapped out noise pollution scenarios under different ship speed limits to see whether the noise level decreased significantly.

In the end, we found that noise pollution is omnipresent in the SRKW critical habitat; the whales are almost never freed from some sort of interference in their communication calls. Additionally, we found that no realistic speed limit reduces noise significantly. What does this mean for the SRKW? Mostly, our research reiterates that DFO has done a poor job in protecting the home of this endangered species. However, we believe that future research into alternate shipping routes and identification of specific months or times of day for shipping that avoid critical killer whale feeding and breeding times and areas could lead to successful SRKW protection.

Our poster we presented to the EOSC faculty. You should be able to read it by clicking on it.

See our blog for more info on our project:-)

Carnivorous Furniture Powered by Bacteria

Robert Krulwich, in his blog ‘Krulwich Wonders’, recently  wrote about the fascinating and morbid creations of designers James Auger and Jimmy Loizeau. These creations are typical furniture such as a clock, lamp, and table, but are built to have a carnivorous streak.

James Auger and Dr. Chris Melhuish speak about their creations:

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During the development of a digital wall clock powered by flies, Auger and Loizeau drew inspiration from carnivorous plants that trapped insects and consumed them for nutrients. A trap mechanism, which consisted of a slowly rolling sticky conveyor belt, deposited any unfortunate flies into a microbial fuel cell sitting below the belt. The display of the clock was powered entirely by the energy obtained from the digestion of the flies. However, the conveyor belt motor was powered by battery or through an outlet, since the trap did not catch enough flies to power the motor.

A microbial fuel cell is a chamber that contains bacteria, which consume organic material. During consumption, the bacteria release electrons that the fuel cell channels to generate electricity and power whatever is connected to the cell. Microbial fuel cells have also been used to generate power from algae.

A dirt-based microbial fuel cell (MFC) - By: Engineering for Change via Flickr

Dr. Chris Melhuish and his team at the Bristol Robotic Laboratory have utilized microbial fuel cells to power robots called ‘EcoBots’. These robots are outfitted with microbial fuel cells that created a system, similar to digestion, which effectively extracted and used energy from the environment. For example, dead flies fed to the robot were digested by bacteria in the microbial fuel cells, the ‘gut’ of the robot, to provide energy for motion. Presently, the fuel cells are only capable of powering short spurts of movement. The research team aims to develop microbial fuel cells that are able to power continuous movement.

With the prices of oil rising, this technology is definitely important in the development of an alternative and renewable fuel source. Personally, I would not mind a fly powered clock, but I would steer clear of a mouse consuming coffee table.

Feces combats Clostridium difficile

Clostridium difficile or C-diff is a bacterium that 5-10% of the population have in their intestine as part of their normal flora, which is the intestinal composition of ‘good’ usually non-disease causing bacteria. In hospital settings, the amount of people that have C-diff in their intestine rises to 25%. C-diff is of particular concern in hospitals since there is a greater potential for patient to patient C-diff spread.


Clostridium difficile - By: AJC1 via flickr

Some antibiotic treatments destroy the normal flora, however C-diff is a spore former, so it is not killed by many antibiotics. The absence of most of the normal flora allows for C-diff to germinate and grow – this produces toxins!  These toxins damage the mucus lining of the colon, which results in ulcers and layers of debris that leads to frequent diarrhea. The disease, called pseudomembranous colitis, can be fatal but is treatable with the powerful and costly antibiotic, Vancomycin. Despite treatment, there is still a high relapse rate of 10-20%.

A news article from The Seattle Times published that American doctors, including Dr. Lawrence Brandt and Dr. Christina Surawicz, have transplanted feces from a healthy person to a sick patient’s colon to combat C-diff and repopulate normal flora. Rest assured, the donors of the stool transplant are close relatives of the sick patient. The doctors of the news article claimed to have so far met success with this unconventional treatment. However, fecal transplants are not widespread and Dr. Brandt even noted that methods among doctors are inconsistent.

Locally, the CBC published an article indicating that the BC Fraser Health Authority had initially barred fecal transplants due to lack of study. I feel that this is currently reasonable until a greater amount of clinical trials are published. Of the published small scale case studies, one in 2009 obtained a  ~73% success rate with fecal transplants and later in 2010 another study posted 100% success. There is also a full clinical trial underway from the University Health Network in Toronto.

Dr. Jeanne Keegan-Henry speaks on fecal transplants:
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In my opinion, one of the issues of fecal transplants is that most of the published research is within the last two years. The long term effects of introducing a different composition of bacteria and potentially other things into a sick patient are not known. If full clinical trials continue to be successful, an antibiotic free treatment for C-diff would not only ease costs for patients, but also slow the development of multi-antibiotic resistant superbugs.

The Vast Field of Biomechatronics

Biomechatronics – one of science’s most rapidly developing areas –  is a  field that encompasses biology, mechanics and electronics. Examples of inventions that have sprouted from this field include, ECG’s, surgical robotics, medical cameras, and other body monitoring devices. One of the most recent discoveries in this field have sprouted from combinations of robotics and neuroscience, in which researchers have been working to develop prosthetic limbs that render the user under complete control of its functions – solely relying on the individual’s own cognitive processes.

One of the most notable breakthrough stories that I read about belongs to that of Pierpaolo Petruzzellio. Petruzzellio, an Italian man, lost his left arm in a car accident at the age of 25. Scientists in Rome quickly grasped this unfortunate event in Petruzzellio’s life as an opportunity to test their latest technology in hopes of giving him the chance of gaining a fully functional arm again. Electrodes were placed on the nerves that remained in Petruzzellio’s forearm, and  were then attached to a robotic arm through a network of cables and wires. Though the arm was not directly attached to his body, Petruzzellio claimed after a month he began to feel sensations in the artificial limb –  almost as if he had a real arm again. All this in consideration, the process was certainly not easy. It took Petruzzellio about a month of consistent focus and determination to begin to control the robotic arm to form even the most primitive of hand gestures, (wiggling of fingers, clenched fists, etc) and even then they were still shaky and took a great amount of mental control. Nonetheless, the dexterity exhibited by Petruzzellio was something that had never been witnessed before in this field of science.

Though this is undoubtedly an amazing advancement in biomechatronic science, one may wonder – where can the possibilities end? Now that scientists are well on their way to providing fully functional, consciously controlled prosthetics, what’s not to stop them from further developing these projects – branching out from aiding the disabled, to augmenting the abilities of normal, healthy humans? What if scientists are able to create robotic legs, capable of running never before seen speeds and carrying inhuman strength? What if 10 years down the road, humans were capable of being mechanically fitted to possess multiple limbs? In sports, could these mechanical advantages for the disabled be deemed appropriate?

Where should the line be drawn? As long as Arnold Schwarzenegger as Terminator doesn’t show up anytime soon, I think I’ll be all right.

Biomechatronics taken too far?

Check out this amazing video depicting the science behind Petruzzellio’s artificial limb, and his experiences.