Category Archives: Science Communication

Hide and Go Seek: HIV vs Mathematical Model

Math may help overcome ‘sleeper cell’ hurdle in HIV treatment
New research on HIV treatment is important for helping the 33 millionpeople who are affected in North America, Sub-Saharan Africa and the rest of the world.HIV is a Human immunodeficiency virus.  It is a condition in humans where the infection causes the immune system to fail, leading to life threatening infections and diseases.


The HIV virus can survive in two places in the body; inside cells or free floating in the blood.Inside a cell, the HIV virus has two options it could begin making copies of itself using the cells own DNA xerox machine, once enough copies are made the new viruses can break out of the cell and go on to infect other cells in the body. Other times the virus may simply hide out in the cell in a dormant phase. This dormant phase is what makes antiretroviral medication less than 100% effective. The medication can only target the free viruses and the ones that are making copies. The ones that are hiding could become active later on with out any warning.

See podcast for more on dormant cells.

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The unpredictable activation of dormant cells led to some unique research by mathematicians at the University of British Columbia. They have used a mathematical model to track and predict how virus levels change in a patient when the dormant cells wake up. The research shows that these cells don’t wake up because of a trigger (like failing drug treatment) but are due to random activations.

See Video for more on the mathematical model.

HIV can be detected through the screening of the blood. HIV infection occurs by the transfer of bodily fluids such as breast milk, blood, semen, vaginal fluid and pre-ejaculate. The most common routes of transmission of the infection is through unprotected sex, contaminated needles, breast milk and transmission from an infected mother to her child at birth.

The mechanism behind HIV is that it primarily infects the cells in the human immune system (T cells, white blood cells, macrophages and dendritic cells) which essentially protect the human body from infections. CD4+ T cells are a type of white blood cell that guides other white blood cells to fight infections. HIV infection leads to low levels of these CD4+ T cells, through three main mechanisms:
  1. direct viral killing of infected cells
  2. increased suicide rates in infected cells (most cells in our body are programmed to self destruct when they get old)
  3. killing of infected CD4+ T cells by CD8 cytotoxic lymphocytes that recognize infected cells.  These are like cops that hunt down the infected cells.

When the level of CD4+ T cells declines to a critical level, the protection provided by white blood cells is lost, and the body becomes more susceptible to infections. This is commonly known as AIDS.

Computer model brings better understanding of complex ecosystems



The spheres and colors represent the various species and trophic levels respectively, in Nevada Lakes, USA. (Picture Credits: Harper et al. 2005).

Numbers are numbing and data are messy. “Visualization tools can help untangle complexity,” says Eric Berlow—ecologist at Sierra Nevada Research Institute in California.  Good visualizations can bring out the details, organize information, and allow scientists to see data in a different way. A computer model called “Niche Model” emerged in the year 2000. It was developed by researchers of the applied mathematics department at Cornell University, Williams and Martinez. Before the model, many ecologists base their theories on “sharply focused” ecosystems with less species, to avoid “clutters” in their study.  However, this was problematic since it risks oversimplifying real-world phenomena.

Since 2000, Niche Model injected a healthy dose of complexity into the field of ecology and conservation biology research. By embracing the complexity, ecologists can now generate more accurate predictions that mimic real ecosystems.

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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.

Predator Computer Program Tracks Human Face Better than You

Now that the class has finished their interviews and has begun to assemble their footage, depending on how they conducted their interview it’s likely that some surprises may appear in the editing room. I know from personal experience now that it is difficult being a professional cinematographer. Fitting the subject into the frame of the shot just right and following their movement is not as easy as one would think.

But what if you had a camera that could do all this by itself and you merely had to press record? Zdenek Kalal, a PhD student at the University of Surrey in England, has just finished research that could make this a reality. He has developed a real time tracking program that unlike previous visual identification systems learns over time. That is, it can learn what the subject in question looks like at various angles and distances and actually gets more accurate over time. Affectionately named Predator, it promises to be the next generation of visual recognition technology.

The below video from the creator Mr. Kalal himself shows the program in action and provides an excellent introduction to the technology. Incidentally he also provides a fine example of how to effectively present research to the public.

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As Mr. Kalal explains, the possible uses for the device go beyond simple facial recognition, although in the context of this class that would certainly be the most welcome. How simple would it be to tell Predator what to focus on, and then let a motorized camera automatically track your subject while you are free to carry out the interview unencumbered. Even in the context of large studio films I would not be surprised to learn that directors are eager to experiment with it. In the realm of science there are also several possibilities. The example noted in the video centres around animal research. The use visual recognition software could revolutionalize the field of wildlife biology. Studies of much larger scale could be completed by using cameras mounted in strategic locations, rather than relying on scientists heading out into the field to do manual observations.

Here is a link to the original press release from the University of Surrey, whose creation  process is yet another area of science that we are now familiar with thanks to Science 300.

The Gulf of Mexico Still Far From Recovery

A video of the BP Spill Explained: YouTube Preview Image

The Gulf of Mexico Oil Spill, also known as the BP Spill occurred on April 20, 2010 is known as the largest accidental marine oil spill in history[1]. The cleanup was done by burning the oil, and using chemical dispersant as well as oil-eating microbes. Microbes are small unicellular organisms. Alcanivorax borkumensis use oil as food[2]. By August 2010, most of the oil on the surface of the ocean was dissipated[3], but about 79% of the oil was still under the surface[4]. The BP (British Petroleum) compensation czar claimed that the Gulf would be recovered by 2012, however, research conducted by marine biologist Dr. Joye demonstrated that the oil is not degrading fast enough[5].

Joye’s research included 5 expeditions using deep-dives into the Gulf of Mexico near the oil spill to collect 250 samples from the ocean-floor and water columns. Her study found that much of the oil spill on the ocean floor and the water columns were from the BP spill. This was done by chemically fingerprinting the oil, and testing the samples in labs.

According to Joye’s findings, the oil-eating microbes that were thought to degrade most of the oil spill consumed about 10% of the oil spill. The rest are dispersed throughout the Gulf as small droplets, which can’t be seen on the surface, but a large amount of the oil droplets sank to the ocean-floor. Moreover, the mucous secretion from the oil-eating microbes which also contain oil sank to the bottom, on top of many bottom-dwelling sea creatures, such as starfish and crabs. Joye’s estimate of the total amount of oil leaked into the ocean is equivalent to 1.5 and 3 million barrels, and she thinks that the recovery will be much slower than what the BP czar claimed.

Oil on Floor

A wall of methane ice on the bottom of the Gulf of Mexico - Woods Hole Oceanographic Institution

The damage done by this accident propose a much long-term effect on the fragile marine ecosystem as well as the marsh in Louisiana. Before reading about Joye’s research, I used to believe that the oil spill was recovering fast, mostly by the oil-munching microbes. However, the pictures and the data collected from the bottom of the ocean by Joye changed my opinion, that under the turquoise-blue surface of the ocean, the sea-floor is still struggling to recover.

The long-term public health implications from this spill is unknown, and still needs to be studied.

An Interview with Dr. Samantha Joye at the UGA Oil Spill Symposium on 26th of January 2011:

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[1] http://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill

[2] http://www.scientificamerican.com/article.cfm?id=scientists-break-down-oil

[3] http://www.nytimes.com/2010/07/28/us/28spill.html?_r=2&hp

[4] http://www.bloomberg.com/news/2010-08-17/scientists-say-79-of-spilled-oil-may-remain-challenging-administration.html

[5] http://ca.news.yahoo.com/gulf-mexico-bottom-shows-little-sign-recovery-bp-20110219-152454-973.html