Monthly Archives: April 2012

Modern human diseases and demographics

Tumultuous effects resulted and continue to result from the massive mixing of the world’s biota when European ships reconnected the American continent to the rest of the world.  Mann traced several of the cascading consequences of “the biggest ecological convulsion since the death of the dinosaurs.”
The first momentous change came from microbial exchange—20 lethal diseases came from Europe to the Americas while only one (syphilis) went the other way.  North America, which had been largely cleared by natives with fire and agriculture, reforested when two-thirds to 95% of the native inhabitants died from European diseases—”the greatest demographic catastrophe in human history.”  That huge reforesting drew down atmospheric carbon dioxide and Europe’s “Little Ice Age” (1550-1800) apparently resulted.
Meanwhile the mountain of silver at Potosí, Bolivia, vastly enriched Europe, which “went shopping” worldwide.  Trading ships coursed the world’s oceans.  One artifact picked up from Peru was the potato—a single variety of the  6,000 available.  When potatoes in Europe turned out to provide four times the amount of food per acre as wheat, the previously routine famines came to an end, population soared, governments became more stable, and they began building global empires.  After 1843 guano shipped by the ton from coastal Peru for fertilizer introduced high-input agriculture.  In Ireland 40% of the exploding population ate only potatoes.  Around 1844 a potato blight arrived from Mexico, and a million Irish died in the Great Famine and a million more emigrated.
In China, which has no large lakes and only two major rivers, agriculture had been limited to two wet regions where rice could be grown.  Two imports from America—maize and sweet potato—could be farmed in dry lands.  As in Europe, population went up.  Vast areas were terraced as Han farmers pushed westward as far as the Mongolian desert.  In heavy rains the terraces melted into the streams, and silt built up in the lowlands, elevating the rivers as much as 40 feet above the surrounding terrain, so when they flooded, millions died.  “A Katrina per month for 100 years,” as one Chinese meteorologist described it.  The constant calamities weakened the government, and China became ripe for foreign colonial takeover.
In America two imported diseases—malaria and yellow fever—were selective in who they killed.  Europeans died in huge numbers, but Africans were one-tenth as susceptible, and so slavery replaced traditional indentured servitude in all the warm regions that favored mosquito-borne diseases.  As one result, four times as many Africans as Europeans crossed the Atlantic and began mixing with the remaining native Americans, giving rise to an endless variety of racial blends and accompanying vitality throughout the Americas.
During the Q & A, Mann described a potential fresh eco-convulsion-in-waiting.  “There is an area in southeast Asia roughly the size of Great Britain that is a single giant rubber plantation.”  Where rubber trees originally came from in the Amazon there is now a rubber tree leaf-blight that is starting to spread in Asia.  “You could lose all the rubber trees in three to six months.  It would be the biggest deforestation in a long time.”  The entire auto industry, he added, depends on just-in-time delivery of rubber.
Stuart Brand’s summary of Charles C. Mann’s talk at The Longnow Foundation in April 2012. I decided to post it because it is one of the most eloquently articulated account of the modern history of Homo sapiens.

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Filed under Anthropology, Evolution, Human Evolution

Phylo: Crowdsourcing BIOINFORMATICS and GENOMICS

For many reasons multiple species DNA alignment is a hard problem. One reason it is hard is because as evolutionary relationship between organisms increase, the similarities in their DNA sequence decrease. Many times we encounter gaps and duplications that make accurate alignment very difficult.

Computer algorithms are getting better (compare CLUSTAL-W to  Clustal Omega), it is still pretty darn difficult to accurately align multiple species. A lot of time and effort is needed to manually inspect alignments performed even by the best multiple species aligner. A handful of scientists can only take it so far…so, crowdsourcing helps here.

One can use an algorithm to perform multiple species alignments of multiple genomes. These alignments can then be made publicly available to public such that they can, in their leisure, improve them by manually intervention. Recently, I came across PHYLO which is a GAME, yes a  GAME!!!! in which multiple species alignments of human genome that are potentially linked to various genetic disorders, such as breast cancer can be manually curated by the public. “Every alignment is received, analyzed, and stored in a database, where it will eventually be re-introduced back into the global alignment as an optimization.”

This is a wonderful opportunity for the public to learn a little about bioinformatics and to understand about evolution. So folks, substitute your AngryBirds with Phylo and help yourself increase your chances of living longer by helping the scientific community move closer towards finding ‘cures’ for these diseases.

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Filed under My Life My Thoughts