Archive for August, 2008

Geography and Genes

Published by Garry Peterson on August 18, 2008 in Visualization. 1 Comment

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.

Agricultural involution in the IJsselmeer, Netherlands

Published by Garry Peterson on August 9, 2008 in Visualization. 0 Comments

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.

Archetypical landscape of the USA

Published by Garry Peterson on August 7, 2008 in Visualization. 0 Comments

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.

Short Links: Gorillas, drunky shrews, and jellyfish

Published by Garry Peterson on August 6, 2008 in General. 0 Comments

Three nature stories from the New York Times:

In the Congo Republic a survey has discovered a large population (125 000) of Western lowland gorillas.

Trove of Endangered Gorillas Found in Africa

The survey was conducted by the Wildlife Conservation Society and local researchers in largely unstudied terrain, including a swampy region nicknamed the “green abyss” by the first biologists to cross it. Dr. Steven E. Sanderson, the president of the society, marveled at the scope of what the survey revealed. “The message from our community is so often one of despair,” he said. “While we don’t want to relax our concern, it’s just great to discover that these animals are doing well.”

It’s Always Happy Hour for Several Species in Malaysian Rain Forest

German scientists have discovered that seven species of small mammals in the rain forests of western Malaysia drink fermented palm nectar on a regular basis. For several of the species, including the pen-tailed tree shrew, the nectar, which can have an alcohol content approaching that of beer, is the major food source — meaning they are chronic drinkers.

Oceanic food webs shifting to dominance by jellyfish, due to overfishing of top predators, and likely coastal eutrophication and climate change.

Stinging Tentacles Offer Hint of Oceans’ Decline

From Spain to New York, to Australia, Japan and Hawaii, jellyfish are becoming more numerous and more widespread, and they are showing up in places where they have rarely been seen before, scientists say. The faceless marauders are stinging children blithely bathing on summer vacations, forcing beaches to close and clogging fishing nets.

But while jellyfish invasions are a nuisance to tourists and a hardship to fishermen, for scientists they are a source of more profound alarm, a signal of the declining health of the world’s oceans.

“These jellyfish near shore are a message the sea is sending us saying, ‘Look how badly you are treating me,’ ” said Dr. Josep-María Gili, a leading jellyfish expert, who has studied them at the Institute of Marine Sciences of the Spanish National Research Council in Barcelona for more than 20 years.

Mapping global wind energy potential

Published by Garry Peterson on August 6, 2008 in Visualization. 0 Comments

From EO Newsroom: Global Ocean Wind Energy Potential

global ocean wind energy

and from Archer, C. L. and M. Z. Jacobson, 2005: Evaluation of global windpower. J. Geophys. Res.-Atm., 110, D12110, doi:10.1029/2004JD005462.


Bike rack art

Published by Garry Peterson on August 4, 2008 in Design and General. 0 Comments

Musician and artist David Byrne is a judge for the bike rack design contest in New York City.  The entries were asked to be as creative as possible while recognizing the requirements of “security, ease of installation and maintenance, and efficient use of space”.  The Wall Street Joournal video to above, shows some racks Byrne was inspired to create himself.  More entries are here.