Wednesday, July 07, 2010

Who's watching your dishwasher

I followed a link in this Seth Godin blog post to a video of a presentation given by Tim O'Reilly at a recent conference. The theme of the talk was the importance of data and data accessibility to future web based applications. I did not watch the whole thing, but a point he made about 10 minutes into the talk really struck me. He was talking about smart metering of electricity consumption.

Smart metering has been around for a while and is touted as a way to promote energy conservation by allowing consumers to observe their energy consumption habits. More sophisticated versions would also provide utility companies the information and control needed to allow them to balance loads and control levels of peak demand. In order for utility companies to gain information about consumption of individual appliances it was believed that each appliance was going to need to have some connectivity to the Internet, possibly in the form of unique IP addresses.

The cool thing that O'Reilly said was that people studying data from smart meters have discovered that each type of appliance and even appliances of the same type from different manufacturers have distinct energy consumption profiles. This fact along, with the appropriate reference dataset would allow data miners to identify the type of equipment being used from raw energy consumption data without any connectivity to the Internet or unique identifiers for each piece of equipment.

As O'Reilly himself states in his talk, there are clearly privacy implications for this use of the energy consumption data. However, the more interesting aspect is that it is yet another example of the unanticipated consequences of our ever increasing ability to collect, store and share vast quantities of information.

Thursday, July 01, 2010

14 inch teeth!!

Fossil remains of a predatory whale related to the modern sperm whale were recently found in Peru. Their teeth were up to 36 cm (more than 14 inches) long.

The full report is behind a subscription barrier but a summary can be read here.

Tuesday, June 22, 2010

Eating oil

The productivity of modern industrial agriculture is a phenomenal technological achievement. The amount of food produced per unit of arable land has increased dramatically over the past 40 years. But, this productivity comes at a cost. Current high yield methods are resource intensive and are completely dependent on substantial inputs of fossil fuel. in a 2008 article in the New York Time Magazine author and journalist Michael Pollan puts it bluntly
"When we eat from the industrial-food system, we are eating oil and spewing greenhouse gasses."

Carbon is released into the atmosphere during multiple steps of the modern industrial food production process. CO2 sources include:

  • Release of carbon during the clearing and tilling of land
  • Production of synthetic fertilizers
  • Use of petroleum based pesticides
  • Energy consumed during the transformation of farm products into the highly processed products that makes up a large fraction of the modern american diet
  • Long distance transportation of food from farmer to consumer
  • and the fuel used by heavy farm equipment at multiple stages of the process

In fact, food production is second only to transportation for its relative impact on our carbon footprint. As a result, chainging our food consumption habits will help mitigate the impacts of climate change.

Tuesday, May 25, 2010


The discovery of antibiotics is one of the most significant medical accomplishments of the last century. Their impact has been profound. Along with improvements in sanitation and vaccinations, the use of antibiotics remains at the forefront of our largely successful efforts to control infectious diseases. As with PCR, we owe the availability of antibiotics to evolution. They are not invented, they are produced naturally by a variety of different organisms.

The modern era of control of bacterial infections began in 1927 with the discovery by Alexander Fleming that extracts from the mold Penicillium notatum lysed bacterial cells. He was not able to isolate the active compound but gave it the name Penicillin after the mold’s genus. The active compound was eventually isolated and developed into a therapy in the early 1940’s by a groups led by Chan and Florey. For their efforts, they shared the 1945 nobel prize for physiology and medicine with Fleming. The receipt of the Nobel Prize just a few short years after the introduction of penicillin as a drug speaks to the impact this medication had.

Many new antibiotics have been introduced since the 1940's but Penicillin and penicillin like antibiotics remain in wide use, comprising almost 20% of all antibiotics manufactured.

Image source

Tuesday, May 18, 2010


From the CDC website on Obesity
American society has become 'obesogenic,' characterized by environments that promote increased food intake, nonhealthful foods, and physical inactivity.
In 2007-2008 almost 70% of representative sample of 5,555 adults from the US population were found to be overweight or obese. 33% were found to be obese (defined as a BMI of 30 or greater)1.

1 Flegal et al 2010. Prevalence and Trends in Obesity Among US Adults, 1999-2008. JAMA 303:235-241

Monday, May 17, 2010

Flavobacterium columnare

I study the bacteria Flavobacterium columnare. It is a fresh water bacteria found all over the world. It is an opportunistic fish pathogen and is the cause of Columnaris Disease (CD). It infects many commercially important fish species. Outbreaks in aquaculture facilities are common. Costs associated with CD are high and represent a major barrier to the development of commercially viable aquaculture enterprises.

Outbreaks are brought on by stress and can occur suddenly. Mortality rates can reach 100%. The most virulent strains F. columnare kill susceptible fish within 24 to 48 hours, leaving little time for treatment.

CD is common in tropical aquaria where it is called by various names including, fin rot, tail rot and cotton mouth. These are frequently discussed on websites for aquaria hobbyist. The bacteria responsible is often identified as Flexibacter columnaris, an obsolete genus and species name replaced in the mid 1990. The characteristic fuzzy white growth the bacteria cause, often results in hobbyists mistaking it for a fungal infection.

CD also effects wild fish stocks. Outbreaks usually occur in the spring as the water warms. These outbreaks can be quite dramatic with hundreds or even thousands of moribund fish washing ashore covered with lesions. In less populous areas, these outbreaks go unnoticed. When they occur in lakes in populated areas, the fish die-offs make the news.

No one likes to see (or smell) tons of dead fish washing up on their shore.

Thursday, May 13, 2010

China in Africa

Howard French has an article in the Atlantic describing the significant investments China is making to build infrastructure across Africa. Chinese investment in Africa currently exceeds $100 billion annually. China’s approach to development differs from the west. The west provides support primarily in the form of grants and heavily subsidized loans. China’s focus is on trade and investment in commercially viable enterprises.

In this model, China provides infrastructure development to Africa. In return, China gets access to the continents vast natural resources including iron, cobalt, copper and other minerals needed to feed its enormous manufacturing based economy.

The key question is if this openly capitalistic, investment based approach can offer sustainable development for Africa. Or, is China gaining access to the continents mineral resource for short term unsustained infrastructure improvements.

History shows that this concern is well founded. French illustrates this by describing a trip on the poorly maintained Tazara train line in Tanzania. The Tazara train line was built by the Chinese in the early 1970’s. It is as an example how mismanagement and corruption led to this big past investment failing to realize its potential.

Simply building infrastructure is not enough. In order to take full advantage of physical infrastructure improvements, investments to train the human capital needed to maintain the infrastructure is also needed. It is not necessarily the obligation of foreign investors such as China to do this, but if the goal is to help the continent develop, it is essential.

It all boils down to educating to empower the local population.

Monday, May 10, 2010

Nature's contribution to modern science

The polymerase chain reaction or PCR is central to much of the molecular biology research performed today. The technique was used for the human genome project, is used as the definitive test to identify many pathogens including H1N1 and is the basis for our understanding of the tree of life. Hundreds of thousands, if not millions of PCR’s are performed every day in labs all over the world. The enzyme used for PCR is called Taq Polymerase1. It is at the heart of the PCR reaction and it was not engineered by man. Rather, it evolved billions of years ago. It is a beautiful example of natures power to innovate.

Polymerases are a class of enzyme that catalyze the synthesis of a chain, or polymer, from component parts. Taq polymerase is a DNA polymerase, catalyzing the syntheses of DNA from nucleic acids. All living things have to have at least one DNA polymerase in order to synthesize the DNA required for growth and reproduction.

The exponential amplification characteristic of PCR stems from ability to repeat the reaction steps over an over again by cycling the reaction through a series of temperatures. These temperature steps include one at near boiling. This high temperature separates the double strands of DNA allowing each strand to be used as a template to synthesis more DNA.

Most enzymes (including most DNA polymerases) are not heat stable. They denature when heated and lose their activity, even after they are cooled back down. Taq polymerase isolated from the thermophilic bacteria Thermus aquaticus retains it activity after being heated to near boiling (95 °C). It is not active at 95 °C, but renatures and regains its activity upon being cooled. The ability of Taq polymerase it to remain active after repeatedly being heated allows the cycling of the PCR to create billions of copies of a target sequence from a single template using reagents added at the begining of the reaction.

1This was the first theromostable polymerase to be widely used. In the more than 25 years since its introduction, other heat stable polymerases have been introduced.

*last edited 11 May 2010 - minor edits and links added

Monday, May 03, 2010

clearly stated target outcomes are needed to form good policy

In my current job, I have participated in the planning and writing of several multi-million dollar grants. On more than one occasion I have been struck by how meager the planning process was. Programs are developed with little in the way of clear objectives, evaluation metrics or paths to sustainability. Of course, this problem is not unusual as Jeffery D. Sachs explains in the May issue of Scientific American:

During 14 months of debate over health care, the administration did not put forward a clear, analytical policy white paper on the aims, methods and expected results of the proposed reforms. Only the Congressional Budget Office’s budget scoring of legislative proposals was even partly systematic; no comparable independent analysis exists on other substantive issues. The actual health consequences of the legislation were never reviewed or debated coherently.

Thursday, April 22, 2010

Wednesday, April 21, 2010

Green glowing frogs detect pollution

Just came across this article from last December about engineering tadpoles to express green fluorescent protein when exposed to pollutants. A strength this approach has over more traditional techniques is that the tadpoles only respond to bioavailable forms of target toxins.

Since this is fluorescence not luminescence, the detection would require at minimum a special light source and a filter. My first thought when seeing this was to wonder how they detect the fluorescence. According to the researchers this turned out to be “nontrivial.”

"Tadpoles aren't just going to sit still while you measure them. They're usually off and running."

Product literature available at the website of the company the researchers founded, WatchFrog, says that the method can be used to detect hormonal disruptors and heavy metals.

Tuesday, April 20, 2010

It is a microbial world!

Researchers scouring the world's oceans have been forced to drastically revise estimates for the number of microbial species residing there after a census indicated up to one hundred times the expected diversity may be present.
Qiu 2010. Nature Online