Category Archives: Visualization

Visualization

Geography and Genes

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From the New York Times reporting on an article by Oscar Lao and others in Current Biology:

A genetic map of Europe

The map shows, at right, the location in Europe where each of the sampled populations live and, at left, the genetic relationship between these 23 populations. The map was constructed by Dr. Kayser, Dr. Oscar Lao and others, and appears in an article in Current Biology published on line on August 7.

The genetic map of Europe bears a clear structural similarity to the geographic map. The major genetic differences are between populations of the north and south (the vertical axis of the map shows north-south differences, the horizontal axis those of east-west). The area assigned to each population reflects the amount of genetic variation in it.

…

Data for the map were generated by gene chips programmed to test and analyze 500,000 sites of common variation on the human genome, although only the 300,000 most reliable sites were used for the map. Dr. Kayser’s team tested almost 2,500 people and analyzed the data by correlating the genetic variations in all the subjects. The genetic map is based on the two strongest of these sets of correlations [the principal components used to plot the data above – these explained 31.6% and 17.3%, of the total variation.  The potential geographic basis of these two PCs was supported by a positive correlation (r2 = 0.6) between the genetic and  geographic distances among the samples.].

The gene chips require large amounts of DNA, more than is available in most forensic samples. Dr. Kayser hopes to identify the sites on the human genome which are most diagnostic for European origin. These sites, if reasonably few in number, could be tested for in hair and blood samples, Dr. Kayser said.

Genomic sites that carry the strongest signal of variation among populations may be those influenced by evolutionary change, Dr. Kayser said. Of the 100 strongest sites, 17 are found in the region of the genome that confers lactose tolerance, an adaptation that arose among a cattle herding culture in northern Europe some 5,000 years ago. Most people switch off the lactose digesting gene after weaning, but the cattle herders evidently gained a great survival advantage by keeping the gene switched on through adulthood.

Visualization

Agricultural involution in the IJsselmeer, Netherlands

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NASA Earth Observatory shows agricultural development and divisions on reclaimed land in the man-made IJsselmeer in the Netherlands. Over time the heterogenity of the newly created land shown in the image as fields are divided and land uses have diversified.

NASA image of land reclamation in NL

NASA Earth Observatory explains:

NASA’s Landsat satellites captured repeated images of IJsselmeer, and recorded changes on one such polder, shown in the top-middle part of each image. Landsat 2 took the top picture on September 8, 1980. Landsat 5 took the middle picture on May 23, 1989. Landsat 7 captured the bottom image on July 1, 2006. In these false-color images, red indicates vegetation, and the brighter the red, the more robust the plant life. Water appears navy blue. Pavement and bare soil range in color from pale blue to gray-green.

Visualization

Archetypical landscape of the USA

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Jeff Cardille at the University of Montreal has a project METALAND that is eveloping more sophiticated ways of characterizing landscapes.  He presented some of his work on archetypical landscapes of the USA at the current Ecological Society of America meeting.

Jeff Cardille 17 archetypical landscapes of USA

On Nature’s blog Emma Morris report’s on his talk From the bright green soy field to the rolling blacktop…this land was made for you and me:

What is the typical landscape of the United States? Jeffrey Cardille, of the University of Montreal wondered the same thing. He may be in Montreal now, but he’s from the US of A, and a big Woody Guthrie fan. Guthrie, in his alternative national anthem “This Land is Your Land” invoked the “redwood forests,” the “gulf stream waters” and so on. But could it be that the archetypal US landscape these days is rather a cornfield or a brand new subdivision?

To find out, Cardille used an algorithm called “affinity propagation”, made famous in this Science paper by Frey and Dueck. As Cardille explains, the algorithm is “a way to find representative samples in complex datasets.” In the Science paper, it was used to create clusters of faces the same people out of a sea of photographs. Each cluster was organized around a central exemplar photo.

Cardille used the same method on landscape data from the National Land Cover Data Set, and metrics extracted from the dataset with a program called fragstats. He gridded the lower 48 off into 6 km by 6 km squares and then let the algorithm rip on the data—5% at a time due to computing power limitations.

What emerges on any one of the runs are something like 17 exemplar squares, real chunks of the landscape that best represent the totality of the landscape. Predictably, of the 17 in the run he presented, 13 are human dominated—row crops, clear cuts, urbanizing suburban land, and the like. Two are carefully managed national parks. Just two are more or less running themselves. One of these is a square of the vast shrub-lands of Texas.

Visualization

Using the web to track disease outbreaks

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HealthMap an interesting global health alert system that was recently accounted in a PLoS Medicine article Surveillance Sans Frontières: Internet-Based Emerging Infectious Disease Intelligence and the HealthMap Project (Brownstein et al 2008).  They explain the motivation for the project:

As developed nations continue to strengthen their electronic disease surveillance capacities [1], the parts of the world that are most vulnerable to emerging disease threats still lack essential public health information infrastructure [2,3]. The existing network of traditional surveillance efforts managed by health ministries, public health institutes, multinational agencies, and laboratory and institutional networks has wide gaps in geographic coverage and often suffers from poor and sometimes suppressed information flow across national borders [4]. At the same time, an enormous amount of valuable information about infectious diseases is found in Web-accessible information sources such as discussion sites, disease reporting networks, and news outlets [5,6,7]. These resources can support situational awareness by providing current, highly local information about outbreaks, even from areas relatively invisible to traditional global public health efforts [8]. These data are plagued by a number of potential hazards that must be studied in depth, including false reports (mis- or disinformation) and reporting bias. Yet these data hold tremendous potential to initiate epidemiologic follow-up studies and provide complementary epidemic intelligence context to traditional surveillance sources. This potential is already being realized, as a majority of outbreak verifications currently conducted by the World Health Organization (WHO)’s Global Outbreak Alert and Response Network are triggered by reports from these nontraditional sources [5,6]. Summary Points

In one of the most frequently cited examples [9], early indications of the severe acute respiratory syndrome (SARS) outbreak in Guangdong Province, China, came in November 2002 from a Chinese article that alluded to an unusual increase in emergency department visits with acute respiratory illness [9,10]. This was followed by media reports of a respiratory disease among health care workers in February 2003, all captured by the Public Health Agency of Canada’s Global Public Health Intelligence Network (GPHIN) [10,11,12]. In parallel, online discussions on the ProMED-mail system referred to an outbreak in Guangzhou, well before official government reports were issued [13].

These Web-based data sources not only facilitate early outbreak detection, but also support increasing public awareness of disease outbreaks prior to their formal recognition. Through low-cost and real-time Internet data-mining, combined with openly available and user-friendly technologies, both participation in and access to global disease surveillance are no longer limited to the public health community [14,15]. The availability of Web-based news media provides an alternative public health information source in under-resourced areas. However, the myriad diverse sources of infectious disease information across the Web are not structured or organized; public health officials, nongovernmental organizations, and concerned citizens must routinely search and synthesize a continually growing number of disparate sources in order to use this information. With the aim of creating an integrated global view of emerging infections based not only on traditional public health datasets but rather on all available information sources, we developed HealthMap, a freely accessible, automated electronic information system for organizing data on outbreaks according to geography, time, and infectious disease agent [16].

Wired news writes:

HealthMap … creates machine-readable public health information from the text indexed by Google News, World Health Organization updates and online listserv discussions.

While aimed at public health workers, HealthMap is also usable by the general public. It locates the outbreaks on a world map and creates a color-coding system that indicates the severity of an outbreak on the basis of news reportage about it. Users of the site can then analyze and visualize the data, gaining unprecedented views of disease outbreaks.

By doing it all with publicly available news sources and low operating costs, the service itself remains free. After a small-scale launch in 2006, the site’s model and potential attracted a $450,000 grant last year from Google.org’s Predict and Prevent Initiative, which is focused on emerging infectious diseases.

It would be great if a similar systems could be used to map and monitor environmental change.

Regime Shifts, Visualization

Algal Bloom along the Coast of China

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There has been a lot of news coverage of the large coastal algal bloom at China’s Olympic sailing site in Qingdao. The Chinese government claims the bloom is now under control.

NASA’s Earth Observatory has published some remote sensed images of the bloom from MODIS:
MODIS comparison of algal bloom

On June 28, 2008, the Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA’s Aqua satellite captured these images of Qingdao and the bay of Jiaozhou Wan. The top image is a natural-color image similar to what a digital camera would photograph. The bottom image is a false-color image made from a combination of light visible to human eyes and infrared light our eyes cannot see. In this image, vegetation appears vibrant green, including the strips of algae floating in the bay and in the nearby coastal waters.

These images show the bay at the beginning of a local cleanup effort. (Daily images of the area are available from the MODIS Rapid Response Team.)

Visualization

Slow ecological art

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On Pruned Alexander Trevi describes the sculptor David Nash‘s art created from following the movement of a wooden boulder down a stream. Nash tried to use the river to move the wood to his studio, and when it became stuck he documented the movement of the wooden boulder downstream. The 25-Year Riverine Journey of a Wooden Boulder Carved out of a Felled 200-Year-Old Oak Tree:

“For 25 years,” Nash writes, “I have followed its engagement with the weather, gravity and the seasons. It became a stepping-stone into the drama of physical geography. Spheres imply movement and initially I helped it to move, but after a few years I observed it only intervening when absolutely necessary – when it became wedged under a bridge.”

wooden boudler 2

woodenboudler1

The journey is so extraordinary — made more so perhaps by the fact that it’s so well-documented — that we can’t help but quote the rest of Nash’s accounts:

During the first 24 years it moved down stream nine times remaining static for months and years. Sedentary and heavy it would sit bedded in stones animated by the varying water levels and the seasons. Beyond the bridge its position survived many storms, the force of the water spread over the shallow banks did not have the power to shift it. I did not expect it to move into the Dwyryd river in my lifetime.

Then in November 2002 it was gone. The ‘goneness’ was palpable. The storm propelled the boulder 5 kilometres, stopping on a sandbank in the Dwryd estuary. Now tidal, it became very mobile. The high tides around full moon and the new moon moved it every 12 hours to a new place, each placement unique to the consequence of the tide, wind, rain and depth of water.

In January 2003 it disappeared from the estuary but was found again in a marsh. An incoming tide had taken it up a creek, where it stayed for five weeks. The equinox tide of March 19 2003 was high enough to float it back to the estuary where it continued its movement back and forth 3 or 4 kilometres each move.

The wooden boulder was last seen in June 2003 on a sandbank near Ynys Giftan. All creeks and marshes have been searched so it can, only be assumed it has made its way to the sea. It is not lost. It is wherever it is.

Visualization

Visualizing US CO2 emissions

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A neat visualization of CO2 emissions from the Vulcan project. They CO2 levels, which aren’t measured, from fine scale air pollution data and atmospheric models to produce high resolution hourly map of US CO2 emissions. Kevin Gurney posted a visualization of their data on YouTube, in which you can see the daily and seasonal variation in emissions.

via Great Beyond and Andrew Revkin’s DotEarth